CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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All RNAs from the RNAstrand dataset

	All RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. Input for comparative methods consisted of a sequence collection / an alignment containing the query sequence and all sequences from a given seed alignment for an Rfam family identified for the query.
Updated: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 30000
Number of RNA sequences: 1987
Robustness test: no

In the summary below ranks have been assigned only to methods, for which at least 40% of comparisons with other methods is valid (i.e. at least 40% (in case of this ranking: 21) of the comparisons were based on at least 10 predictions for common targets).

The ratio 40% / 60% was chosen in order not to bias methods for which not enough predictions have been collected.

Summary of pairwise comparisons

54 methods predicting RNA secondary structure were compared with each other (thus each method has 53 comparisons with other methods (sum of values from columns "Wins", "Losses", "=" and "?" in each row)).

Legend:

=	draw - it is assigned when both methods have generated >= 10 predictions for common targets if:
	1) the accuracies of their results are statistically not distinguishable (P-value greater than 0.001),
	or
	2) the numbers of base pairs classified to categories True Positivies (TP), True Negatives (TN), False Positivies (FP, including 3 subcategories) and False Negatives (FN) for both methods are the same.
?	two methods cannot be compared ("no winner") - not enough predictions for a given pair of methods (minimum is 10)
N/A	a method for which more than 32 (60%) of comparisons with other methods is invalid (see column "?").

Rank	Method Name	Trained	Wins	Losses	=	?	Predictions attempted	Predictions generated
1	TurboFold(seed)	no	52	1	0	0	1242	51
2	ContextFold	yes	51	2	0	0	1987	1987
2	PETfold_pre2.0(seed)	no	51	2	0	0	1242	1224
4	TurboFold(20)	no	50	2	0	1	642	565
5	CentroidAlifold(seed)	yes	49	4	0	0	1242	706
6	PETfold_pre2.0(20)	no	46	6	0	1	642	639
7	CentroidAlifold(20)	yes	45	6	1	1	642	642
8	CentroidHomfold‑LAST	yes	45	8	0	0	1987	1641
9	PPfold(20)	yes	44	7	1	1	642	558
10	RNAalifold(20)	no	42	10	0	1	642	642
11	MXScarna(seed)	no	42	11	0	0	1242	728
12	MXScarna(20)	no	41	11	0	1	642	642
13	IPknot	yes	39	14	0	0	1987	1972
14	Multilign(20)	no	38	14	0	1	642	534
15	Murlet(20)	yes	36	15	1	1	642	504
16	RNAalifold(seed)	no	36	17	0	0	1242	700
17	CentroidFold	yes	35	17	1	0	1987	1915
18	RNASampler(20)	no	34	18	0	1	642	393
19	Contrafold	yes	34	19	0	0	1987	1973
20	Sfold	no	31	22	0	0	1987	1973
21	Multilign(seed)	no	30	9	0	14	1242	23
22	MaxExpect	yes	30	23	0	0	1987	1973
23	ProbKnot	yes	29	24	0	0	1987	1973
24	Fold	no	27	25	1	0	1987	1973
25	RNASampler(seed)	no	26	24	3	0	1242	98
26	UNAFold	no	26	27	0	0	1987	1987
27	RNAsubopt	no	25	27	1	0	1987	1641
28	RSpredict(20)	no	24	26	2	1	642	642
29	CMfinder(20)	yes	24	28	0	1	642	561
30	PknotsRG	no	23	28	2	0	1987	1868
31	Carnac(20)	no	22	30	0	1	642	642
32	RNAfold	no	22	29	2	0	1987	1973
33	CMfinder(seed)	yes	20	30	3	0	1242	129
34	Afold	no	20	32	1	0	1987	1275
35	HotKnots	no	19	31	3	0	1987	876
36	CRWrnafold	yes	18	34	1	0	1987	1837
37	Pknots	no	17	34	2	0	1987	697
38	McQFold	yes	17	35	1	0	1987	1707
38	RNAshapes	no	17	35	1	0	1987	1588
40	PPfold(seed)	yes	15	37	1	0	1242	63
41	Mastr(20)	yes	14	38	0	1	642	592
42	Murlet(seed)	yes	14	36	3	0	1242	123
43	RNASLOpt	no	14	38	1	0	1987	1543
44	Cylofold	no	13	39	1	0	1987	798
45	RNAwolf	yes	9	43	1	0	1987	1788
46	Vsfold4	no	9	44	0	0	1987	1612
47	Vsfold5	no	7	45	1	0	1987	1602
48	Alterna	no	6	43	4	0	1987	693
49	RDfolder	no	4	48	1	0	1987	693
50	Carnac(seed)	no	3	46	4	0	1242	269
51	MCFold	yes	3	47	3	0	1987	761
52	RSpredict(seed)	no	3	48	2	0	1242	702
53	NanoFolder	yes	1	50	1	1	1987	251
54	Mastr(seed)	yes	0	53	0	0	1242	644

Detailed results of pairwise comparisons between methods

Legend:

+	method on the left scored higher in this pairwise comparison
-	method on the left scored lower in this pairwise comparison
=	draw - it is assigned when both methods have generated >= 10 predictions for common targets if:
	1) the accuracies of their results are statistically not distinguishable (P-value greater than 0.001),
	or
	2) the numbers of base pairs classified to categories True Positivies (TP), True Negatives (TN), False Positivies (FP, including 3 subcategories) and False Negatives (FN) for both methods are the same.
?	two methods cannot be compared ("no winner") - not enough predictions for a given pair of methods (minimum is 10)

P-values were obtained using Wilcoxon signed-rank test taking 2 sets of 40 MCC values obtained for 40 random subsets of 90% of the dataset for each pair of methods. If the P-value is lower than 0.001 and there are at least 10 sequences on which benchmark was performed, the difference between the performance of two methods is assumed to be statistically sound.


TurboFold(seed)		+ TurboFold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.795 PETfold_pre2.0(seed): 0.751 Sensitivity TurboFold(seed): 0.765 PETfold_pre2.0(seed): 0.685 Positive Predictive Value TurboFold(seed): 0.828 PETfold_pre2.0(seed): 0.823 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.791 ContextFold: 0.757 Sensitivity TurboFold(seed): 0.762 ContextFold: 0.732 Positive Predictive Value TurboFold(seed): 0.822 ContextFold: 0.784 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.864 TurboFold(seed): 0.858 Sensitivity TurboFold(20): 0.857 TurboFold(seed): 0.851 Positive Predictive Value TurboFold(20): 0.873 TurboFold(seed): 0.867 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 4.42992852122e-09	+ TurboFold(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.788 CentroidAlifold(seed): 0.767 Sensitivity TurboFold(seed): 0.760 CentroidAlifold(seed): 0.675 Positive Predictive Value TurboFold(seed): 0.819 CentroidAlifold(seed): 0.872 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 7.04732813174e-08	+ TurboFold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 PETfold_pre2.0(20): 0.605 Sensitivity TurboFold(seed): 0.851 PETfold_pre2.0(20): 0.395 Positive Predictive Value TurboFold(seed): 0.867 PETfold_pre2.0(20): 0.929 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 4.00488379386e-09	+ TurboFold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 CentroidAlifold(20): 0.693 Sensitivity TurboFold(seed): 0.851 CentroidAlifold(20): 0.520 Positive Predictive Value TurboFold(seed): 0.867 CentroidAlifold(20): 0.925 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.785 CentroidHomfold‑LAST: 0.762 Sensitivity TurboFold(seed): 0.758 CentroidHomfold‑LAST: 0.686 Positive Predictive Value TurboFold(seed): 0.814 CentroidHomfold‑LAST: 0.848 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs PPfold(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 PPfold(20): 0.582 Sensitivity TurboFold(seed): 0.851 PPfold(20): 0.365 Positive Predictive Value TurboFold(seed): 0.867 PPfold(20): 0.933 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 RNAalifold(20): 0.622 Sensitivity TurboFold(seed): 0.851 RNAalifold(20): 0.435 Positive Predictive Value TurboFold(seed): 0.867 RNAalifold(20): 0.893 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.791 MXScarna(seed): 0.734 Sensitivity TurboFold(seed): 0.762 MXScarna(seed): 0.698 Positive Predictive Value TurboFold(seed): 0.822 MXScarna(seed): 0.773 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 MXScarna(20): 0.840 Sensitivity TurboFold(seed): 0.851 MXScarna(20): 0.817 Positive Predictive Value TurboFold(seed): 0.867 MXScarna(20): 0.865 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ TurboFold(seed) vs IPknot Matthews Correlation Coefficient TurboFold(seed): 0.791 IPknot: 0.726 Sensitivity TurboFold(seed): 0.762 IPknot: 0.705 Positive Predictive Value TurboFold(seed): 0.822 IPknot: 0.750 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.854 Multilign(20): 0.589 Sensitivity TurboFold(seed): 0.846 Multilign(20): 0.433 Positive Predictive Value TurboFold(seed): 0.864 Multilign(20): 0.806 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.902 Murlet(20): 0.628 Sensitivity TurboFold(seed): 0.892 Murlet(20): 0.414 Positive Predictive Value TurboFold(seed): 0.914 Murlet(20): 0.957 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ TurboFold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.788 RNAalifold(seed): 0.688 Sensitivity TurboFold(seed): 0.760 RNAalifold(seed): 0.533 Positive Predictive Value TurboFold(seed): 0.819 RNAalifold(seed): 0.888 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.791 CentroidFold: 0.711 Sensitivity TurboFold(seed): 0.762 CentroidFold: 0.681 Positive Predictive Value TurboFold(seed): 0.822 CentroidFold: 0.743 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 RNASampler(20): 0.571 Sensitivity TurboFold(seed): 0.851 RNASampler(20): 0.345 Positive Predictive Value TurboFold(seed): 0.867 RNASampler(20): 0.950 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.791 Contrafold: 0.704 Sensitivity TurboFold(seed): 0.762 Contrafold: 0.703 Positive Predictive Value TurboFold(seed): 0.822 Contrafold: 0.706 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.791 Sfold: 0.690 Sensitivity TurboFold(seed): 0.762 Sfold: 0.665 Positive Predictive Value TurboFold(seed): 0.822 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.740 Multilign(seed): 0.698 Sensitivity TurboFold(seed): 0.698 Multilign(seed): 0.660 Positive Predictive Value TurboFold(seed): 0.784 Multilign(seed): 0.741 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.791 MaxExpect: 0.681 Sensitivity TurboFold(seed): 0.762 MaxExpect: 0.685 Positive Predictive Value TurboFold(seed): 0.822 MaxExpect: 0.679 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.791 ProbKnot: 0.684 Sensitivity TurboFold(seed): 0.762 ProbKnot: 0.691 Positive Predictive Value TurboFold(seed): 0.822 ProbKnot: 0.678 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.791 Fold: 0.678 Sensitivity TurboFold(seed): 0.762 Fold: 0.686 Positive Predictive Value TurboFold(seed): 0.822 Fold: 0.671 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): 0.825 RNASampler(seed): 0.722 Sensitivity TurboFold(seed): 0.771 RNASampler(seed): 0.582 Positive Predictive Value TurboFold(seed): 0.883 RNASampler(seed): 0.897 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.791 UNAFold: 0.678 Sensitivity TurboFold(seed): 0.762 UNAFold: 0.680 Positive Predictive Value TurboFold(seed): 0.822 UNAFold: 0.679 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.785 RNAsubopt: 0.640 Sensitivity TurboFold(seed): 0.758 RNAsubopt: 0.647 Positive Predictive Value TurboFold(seed): 0.814 RNAsubopt: 0.636 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 RSpredict(20): 0.758 Sensitivity TurboFold(seed): 0.851 RSpredict(20): 0.651 Positive Predictive Value TurboFold(seed): 0.867 RSpredict(20): 0.885 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.08932646657e-08	+ TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 CMfinder(20): 0.650 Sensitivity TurboFold(seed): 0.851 CMfinder(20): 0.500 Positive Predictive Value TurboFold(seed): 0.867 CMfinder(20): 0.849 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ TurboFold(seed) vs PknotsRG Matthews Correlation Coefficient TurboFold(seed): 0.791 PknotsRG: 0.680 Sensitivity TurboFold(seed): 0.762 PknotsRG: 0.688 Positive Predictive Value TurboFold(seed): 0.822 PknotsRG: 0.674 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 Carnac(20): 0.481 Sensitivity TurboFold(seed): 0.851 Carnac(20): 0.276 Positive Predictive Value TurboFold(seed): 0.867 Carnac(20): 0.840 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.791 RNAfold: 0.688 Sensitivity TurboFold(seed): 0.762 RNAfold: 0.693 Positive Predictive Value TurboFold(seed): 0.822 RNAfold: 0.685 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): 0.817 CMfinder(seed): 0.576 Sensitivity TurboFold(seed): 0.766 CMfinder(seed): 0.440 Positive Predictive Value TurboFold(seed): 0.873 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.799 Afold: 0.646 Sensitivity TurboFold(seed): 0.768 Afold: 0.650 Positive Predictive Value TurboFold(seed): 0.832 Afold: 0.644 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.798 HotKnots: 0.740 Sensitivity TurboFold(seed): 0.766 HotKnots: 0.745 Positive Predictive Value TurboFold(seed): 0.835 HotKnots: 0.740 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.791 CRWrnafold: 0.580 Sensitivity TurboFold(seed): 0.762 CRWrnafold: 0.585 Positive Predictive Value TurboFold(seed): 0.822 CRWrnafold: 0.577 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.711 Pknots: 0.628 Sensitivity TurboFold(seed): 0.662 Pknots: 0.632 Positive Predictive Value TurboFold(seed): 0.768 Pknots: 0.630 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.791 McQFold: 0.516 Sensitivity TurboFold(seed): 0.762 McQFold: 0.503 Positive Predictive Value TurboFold(seed): 0.822 McQFold: 0.531 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.782 RNAshapes: 0.643 Sensitivity TurboFold(seed): 0.756 RNAshapes: 0.647 Positive Predictive Value TurboFold(seed): 0.811 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.789 PPfold(seed): 0.687 Sensitivity TurboFold(seed): 0.755 PPfold(seed): 0.565 Positive Predictive Value TurboFold(seed): 0.826 PPfold(seed): 0.836 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 Mastr(20): 0.653 Sensitivity TurboFold(seed): 0.851 Mastr(20): 0.460 Positive Predictive Value TurboFold(seed): 0.867 Mastr(20): 0.931 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.781 Murlet(seed): 0.630 Sensitivity TurboFold(seed): 0.750 Murlet(seed): 0.446 Positive Predictive Value TurboFold(seed): 0.814 Murlet(seed): 0.894 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.785 RNASLOpt: 0.522 Sensitivity TurboFold(seed): 0.758 RNASLOpt: 0.497 Positive Predictive Value TurboFold(seed): 0.814 RNASLOpt: 0.552 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Cylofold Matthews Correlation Coefficient TurboFold(seed): 0.800 Cylofold: 0.653 Sensitivity TurboFold(seed): 0.770 Cylofold: 0.626 Positive Predictive Value TurboFold(seed): 0.833 Cylofold: 0.686 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.791 RNAwolf: 0.422 Sensitivity TurboFold(seed): 0.762 RNAwolf: 0.433 Positive Predictive Value TurboFold(seed): 0.822 RNAwolf: 0.414 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.785 Vsfold4: 0.215 Sensitivity TurboFold(seed): 0.758 Vsfold4: 0.197 Positive Predictive Value TurboFold(seed): 0.814 Vsfold4: 0.239 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.785 Vsfold5: 0.260 Sensitivity TurboFold(seed): 0.758 Vsfold5: 0.250 Positive Predictive Value TurboFold(seed): 0.814 Vsfold5: 0.274 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): 0.720 Alterna: 0.546 Sensitivity TurboFold(seed): 0.663 Alterna: 0.520 Positive Predictive Value TurboFold(seed): 0.786 Alterna: 0.581 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.77766983502e-08	+ TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.720 RDfolder: 0.512 Sensitivity TurboFold(seed): 0.663 RDfolder: 0.453 Positive Predictive Value TurboFold(seed): 0.786 RDfolder: 0.588 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.788 Carnac(seed): 0.431 Sensitivity TurboFold(seed): 0.760 Carnac(seed): 0.207 Positive Predictive Value TurboFold(seed): 0.819 Carnac(seed): 0.897 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.788 MCFold: 0.459 Sensitivity TurboFold(seed): 0.752 MCFold: 0.515 Positive Predictive Value TurboFold(seed): 0.828 MCFold: 0.417 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.788 RSpredict(seed): 0.495 Sensitivity TurboFold(seed): 0.760 RSpredict(seed): 0.378 Positive Predictive Value TurboFold(seed): 0.819 RSpredict(seed): 0.650 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.834 NanoFolder: 0.297 Sensitivity TurboFold(seed): 0.797 NanoFolder: 0.355 Positive Predictive Value TurboFold(seed): 0.874 NanoFolder: 0.254 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.791 Mastr(seed): 0.371 Sensitivity TurboFold(seed): 0.762 Mastr(seed): 0.166 Positive Predictive Value TurboFold(seed): 0.822 Mastr(seed): 0.829 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08
PETfold_pre2.0(seed)	49 TurboFold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.795 PETfold_pre2.0(seed): 0.751 Sensitivity TurboFold(seed): 0.765 PETfold_pre2.0(seed): 0.685 Positive Predictive Value TurboFold(seed): 0.828 PETfold_pre2.0(seed): 0.823 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08		- ContextFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient ContextFold: 0.753 PETfold_pre2.0(seed): 0.741 Sensitivity ContextFold: 0.715 PETfold_pre2.0(seed): 0.675 Positive Predictive Value ContextFold: 0.793 PETfold_pre2.0(seed): 0.814 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.800 TurboFold(20): 0.788 Sensitivity PETfold_pre2.0(seed): 0.728 TurboFold(20): 0.739 Positive Predictive Value PETfold_pre2.0(seed): 0.878 TurboFold(20): 0.841 Number of pairs reference - predicted secondary structure: 549 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.764 CentroidAlifold(seed): 0.752 Sensitivity PETfold_pre2.0(seed): 0.701 CentroidAlifold(seed): 0.628 Positive Predictive Value PETfold_pre2.0(seed): 0.834 CentroidAlifold(seed): 0.901 Number of pairs reference - predicted secondary structure: 688 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 PETfold_pre2.0(20): 0.747 Sensitivity PETfold_pre2.0(seed): 0.729 PETfold_pre2.0(20): 0.692 Positive Predictive Value PETfold_pre2.0(seed): 0.830 PETfold_pre2.0(20): 0.807 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 CentroidAlifold(20): 0.742 Sensitivity PETfold_pre2.0(seed): 0.729 CentroidAlifold(20): 0.619 Positive Predictive Value PETfold_pre2.0(seed): 0.830 CentroidAlifold(20): 0.891 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.733 CentroidHomfold‑LAST: 0.698 Sensitivity PETfold_pre2.0(seed): 0.652 CentroidHomfold‑LAST: 0.558 Positive Predictive Value PETfold_pre2.0(seed): 0.827 CentroidHomfold‑LAST: 0.874 Number of pairs reference - predicted secondary structure: 1128 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.799 PPfold(20): 0.766 Sensitivity PETfold_pre2.0(seed): 0.732 PPfold(20): 0.669 Positive Predictive Value PETfold_pre2.0(seed): 0.873 PPfold(20): 0.879 Number of pairs reference - predicted secondary structure: 542 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 RNAalifold(20): 0.689 Sensitivity PETfold_pre2.0(seed): 0.729 RNAalifold(20): 0.604 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RNAalifold(20): 0.786 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.765 MXScarna(seed): 0.652 Sensitivity PETfold_pre2.0(seed): 0.702 MXScarna(seed): 0.566 Positive Predictive Value PETfold_pre2.0(seed): 0.835 MXScarna(seed): 0.752 Number of pairs reference - predicted secondary structure: 710 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 MXScarna(20): 0.644 Sensitivity PETfold_pre2.0(seed): 0.729 MXScarna(20): 0.586 Positive Predictive Value PETfold_pre2.0(seed): 0.830 MXScarna(20): 0.708 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 IPknot: 0.606 Sensitivity PETfold_pre2.0(seed): 0.675 IPknot: 0.549 Positive Predictive Value PETfold_pre2.0(seed): 0.814 IPknot: 0.669 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.800 Multilign(20): 0.689 Sensitivity PETfold_pre2.0(seed): 0.728 Multilign(20): 0.623 Positive Predictive Value PETfold_pre2.0(seed): 0.879 Multilign(20): 0.764 Number of pairs reference - predicted secondary structure: 519 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.801 Murlet(20): 0.630 Sensitivity PETfold_pre2.0(seed): 0.738 Murlet(20): 0.505 Positive Predictive Value PETfold_pre2.0(seed): 0.869 Murlet(20): 0.786 Number of pairs reference - predicted secondary structure: 499 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.760 RNAalifold(seed): 0.636 Sensitivity PETfold_pre2.0(seed): 0.697 RNAalifold(seed): 0.485 Positive Predictive Value PETfold_pre2.0(seed): 0.829 RNAalifold(seed): 0.834 Number of pairs reference - predicted secondary structure: 682 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.742 CentroidFold: 0.570 Sensitivity PETfold_pre2.0(seed): 0.676 CentroidFold: 0.515 Positive Predictive Value PETfold_pre2.0(seed): 0.815 CentroidFold: 0.632 Number of pairs reference - predicted secondary structure: 1223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.830 RNASampler(20): 0.694 Sensitivity PETfold_pre2.0(seed): 0.766 RNASampler(20): 0.551 Positive Predictive Value PETfold_pre2.0(seed): 0.901 RNASampler(20): 0.876 Number of pairs reference - predicted secondary structure: 380 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 Contrafold: 0.554 Sensitivity PETfold_pre2.0(seed): 0.675 Contrafold: 0.540 Positive Predictive Value PETfold_pre2.0(seed): 0.814 Contrafold: 0.569 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 Sfold: 0.525 Sensitivity PETfold_pre2.0(seed): 0.675 Sfold: 0.475 Positive Predictive Value PETfold_pre2.0(seed): 0.814 Sfold: 0.580 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.757 Multilign(seed): 0.698 Sensitivity PETfold_pre2.0(seed): 0.709 Multilign(seed): 0.660 Positive Predictive Value PETfold_pre2.0(seed): 0.809 Multilign(seed): 0.741 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 MaxExpect: 0.514 Sensitivity PETfold_pre2.0(seed): 0.675 MaxExpect: 0.503 Positive Predictive Value PETfold_pre2.0(seed): 0.814 MaxExpect: 0.526 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 ProbKnot: 0.510 Sensitivity PETfold_pre2.0(seed): 0.675 ProbKnot: 0.506 Positive Predictive Value PETfold_pre2.0(seed): 0.814 ProbKnot: 0.516 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 Fold: 0.490 Sensitivity PETfold_pre2.0(seed): 0.675 Fold: 0.493 Positive Predictive Value PETfold_pre2.0(seed): 0.814 Fold: 0.488 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.813 RNASampler(seed): 0.629 Sensitivity PETfold_pre2.0(seed): 0.728 RNASampler(seed): 0.468 Positive Predictive Value PETfold_pre2.0(seed): 0.910 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 UNAFold: 0.492 Sensitivity PETfold_pre2.0(seed): 0.675 UNAFold: 0.488 Positive Predictive Value PETfold_pre2.0(seed): 0.814 UNAFold: 0.496 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.733 RNAsubopt: 0.523 Sensitivity PETfold_pre2.0(seed): 0.652 RNAsubopt: 0.530 Positive Predictive Value PETfold_pre2.0(seed): 0.827 RNAsubopt: 0.518 Number of pairs reference - predicted secondary structure: 1128 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 RSpredict(20): 0.483 Sensitivity PETfold_pre2.0(seed): 0.729 RSpredict(20): 0.398 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RSpredict(20): 0.587 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.800 CMfinder(20): 0.554 Sensitivity PETfold_pre2.0(seed): 0.729 CMfinder(20): 0.387 Positive Predictive Value PETfold_pre2.0(seed): 0.878 CMfinder(20): 0.796 Number of pairs reference - predicted secondary structure: 545 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.756 PknotsRG: 0.507 Sensitivity PETfold_pre2.0(seed): 0.685 PknotsRG: 0.507 Positive Predictive Value PETfold_pre2.0(seed): 0.835 PknotsRG: 0.509 Number of pairs reference - predicted secondary structure: 1193 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 Carnac(20): 0.522 Sensitivity PETfold_pre2.0(seed): 0.729 Carnac(20): 0.306 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 RNAfold: 0.483 Sensitivity PETfold_pre2.0(seed): 0.675 RNAfold: 0.484 Positive Predictive Value PETfold_pre2.0(seed): 0.814 RNAfold: 0.483 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.764 CMfinder(seed): 0.486 Sensitivity PETfold_pre2.0(seed): 0.661 CMfinder(seed): 0.312 Positive Predictive Value PETfold_pre2.0(seed): 0.882 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.748 Afold: 0.480 Sensitivity PETfold_pre2.0(seed): 0.686 Afold: 0.477 Positive Predictive Value PETfold_pre2.0(seed): 0.815 Afold: 0.484 Number of pairs reference - predicted secondary structure: 699 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 HotKnots: 0.657 Sensitivity PETfold_pre2.0(seed): 0.826 HotKnots: 0.660 Positive Predictive Value PETfold_pre2.0(seed): 0.938 HotKnots: 0.659 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.747 CRWrnafold: 0.486 Sensitivity PETfold_pre2.0(seed): 0.672 CRWrnafold: 0.486 Positive Predictive Value PETfold_pre2.0(seed): 0.832 CRWrnafold: 0.487 Number of pairs reference - predicted secondary structure: 1170 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 Pknots: 0.666 Sensitivity PETfold_pre2.0(seed): 0.870 Pknots: 0.673 Positive Predictive Value PETfold_pre2.0(seed): 0.950 Pknots: 0.663 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 McQFold: 0.478 Sensitivity PETfold_pre2.0(seed): 0.646 McQFold: 0.466 Positive Predictive Value PETfold_pre2.0(seed): 0.827 McQFold: 0.492 Number of pairs reference - predicted secondary structure: 1141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.737 RNAshapes: 0.465 Sensitivity PETfold_pre2.0(seed): 0.657 RNAshapes: 0.462 Positive Predictive Value PETfold_pre2.0(seed): 0.828 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 1095 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.747 PPfold(seed): 0.629 Sensitivity PETfold_pre2.0(seed): 0.693 PPfold(seed): 0.500 Positive Predictive Value PETfold_pre2.0(seed): 0.806 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.752 Mastr(20): 0.301 Sensitivity PETfold_pre2.0(seed): 0.694 Mastr(20): 0.114 Positive Predictive Value PETfold_pre2.0(seed): 0.817 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 576 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.800 Murlet(seed): 0.540 Sensitivity PETfold_pre2.0(seed): 0.740 Murlet(seed): 0.360 Positive Predictive Value PETfold_pre2.0(seed): 0.866 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.747 RNASLOpt: 0.478 Sensitivity PETfold_pre2.0(seed): 0.670 RNASLOpt: 0.452 Positive Predictive Value PETfold_pre2.0(seed): 0.835 RNASLOpt: 0.509 Number of pairs reference - predicted secondary structure: 1059 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.881 Cylofold: 0.580 Sensitivity PETfold_pre2.0(seed): 0.828 Cylofold: 0.568 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Cylofold: 0.598 Number of pairs reference - predicted secondary structure: 464 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 RNAwolf: 0.379 Sensitivity PETfold_pre2.0(seed): 0.646 RNAwolf: 0.393 Positive Predictive Value PETfold_pre2.0(seed): 0.827 RNAwolf: 0.367 Number of pairs reference - predicted secondary structure: 1141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 Vsfold4: 0.345 Sensitivity PETfold_pre2.0(seed): 0.655 Vsfold4: 0.318 Positive Predictive Value PETfold_pre2.0(seed): 0.827 Vsfold4: 0.377 Number of pairs reference - predicted secondary structure: 1113 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 Vsfold5: 0.333 Sensitivity PETfold_pre2.0(seed): 0.656 Vsfold5: 0.317 Positive Predictive Value PETfold_pre2.0(seed): 0.827 Vsfold5: 0.352 Number of pairs reference - predicted secondary structure: 1106 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 Alterna: 0.585 Sensitivity PETfold_pre2.0(seed): 0.870 Alterna: 0.595 Positive Predictive Value PETfold_pre2.0(seed): 0.950 Alterna: 0.582 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 RDfolder: 0.557 Sensitivity PETfold_pre2.0(seed): 0.870 RDfolder: 0.511 Positive Predictive Value PETfold_pre2.0(seed): 0.950 RDfolder: 0.615 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.726 Carnac(seed): 0.245 Sensitivity PETfold_pre2.0(seed): 0.626 Carnac(seed): 0.069 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 267 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.880 MCFold: 0.480 Sensitivity PETfold_pre2.0(seed): 0.828 MCFold: 0.542 Positive Predictive Value PETfold_pre2.0(seed): 0.938 MCFold: 0.431 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.763 RSpredict(seed): 0.364 Sensitivity PETfold_pre2.0(seed): 0.698 RSpredict(seed): 0.224 Positive Predictive Value PETfold_pre2.0(seed): 0.835 RSpredict(seed): 0.594 Number of pairs reference - predicted secondary structure: 684 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.742 NanoFolder: 0.201 Sensitivity PETfold_pre2.0(seed): 0.655 NanoFolder: 0.237 Positive Predictive Value PETfold_pre2.0(seed): 0.841 NanoFolder: 0.173 Number of pairs reference - predicted secondary structure: 188 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.739 Mastr(seed): 0.115 Sensitivity PETfold_pre2.0(seed): 0.656 Mastr(seed): 0.016 Positive Predictive Value PETfold_pre2.0(seed): 0.833 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08
ContextFold	51 TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.791 ContextFold: 0.757 Sensitivity TurboFold(seed): 0.762 ContextFold: 0.732 Positive Predictive Value TurboFold(seed): 0.822 ContextFold: 0.784 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1224 ContextFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient ContextFold: 0.753 PETfold_pre2.0(seed): 0.741 Sensitivity ContextFold: 0.715 PETfold_pre2.0(seed): 0.675 Positive Predictive Value ContextFold: 0.793 PETfold_pre2.0(seed): 0.814 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.863 TurboFold(20): 0.787 Sensitivity ContextFold: 0.823 TurboFold(20): 0.740 Positive Predictive Value ContextFold: 0.906 TurboFold(20): 0.837 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.812 CentroidAlifold(seed): 0.749 Sensitivity ContextFold: 0.774 CentroidAlifold(seed): 0.623 Positive Predictive Value ContextFold: 0.853 CentroidAlifold(seed): 0.901 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PETfold_pre2.0(20) Matthews Correlation Coefficient ContextFold: 0.791 PETfold_pre2.0(20): 0.744 Sensitivity ContextFold: 0.752 PETfold_pre2.0(20): 0.686 Positive Predictive Value ContextFold: 0.832 PETfold_pre2.0(20): 0.807 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidAlifold(20) Matthews Correlation Coefficient ContextFold: 0.791 CentroidAlifold(20): 0.740 Sensitivity ContextFold: 0.752 CentroidAlifold(20): 0.616 Positive Predictive Value ContextFold: 0.832 CentroidAlifold(20): 0.891 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.749 CentroidHomfold‑LAST: 0.669 Sensitivity ContextFold: 0.712 CentroidHomfold‑LAST: 0.527 Positive Predictive Value ContextFold: 0.789 CentroidHomfold‑LAST: 0.850 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PPfold(20) Matthews Correlation Coefficient ContextFold: 0.855 PPfold(20): 0.758 Sensitivity ContextFold: 0.814 PPfold(20): 0.654 Positive Predictive Value ContextFold: 0.898 PPfold(20): 0.879 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.791 RNAalifold(20): 0.687 Sensitivity ContextFold: 0.752 RNAalifold(20): 0.600 Positive Predictive Value ContextFold: 0.832 RNAalifold(20): 0.787 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.812 MXScarna(seed): 0.654 Sensitivity ContextFold: 0.774 MXScarna(seed): 0.568 Positive Predictive Value ContextFold: 0.853 MXScarna(seed): 0.753 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.791 MXScarna(20): 0.647 Sensitivity ContextFold: 0.752 MXScarna(20): 0.589 Positive Predictive Value ContextFold: 0.832 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.687 IPknot: 0.563 Sensitivity ContextFold: 0.650 IPknot: 0.501 Positive Predictive Value ContextFold: 0.727 IPknot: 0.632 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.866 Multilign(20): 0.685 Sensitivity ContextFold: 0.827 Multilign(20): 0.617 Positive Predictive Value ContextFold: 0.908 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.843 Murlet(20): 0.629 Sensitivity ContextFold: 0.804 Murlet(20): 0.503 Positive Predictive Value ContextFold: 0.885 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.803 RNAalifold(seed): 0.634 Sensitivity ContextFold: 0.765 RNAalifold(seed): 0.482 Positive Predictive Value ContextFold: 0.843 RNAalifold(seed): 0.835 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.707 CentroidFold: 0.534 Sensitivity ContextFold: 0.670 CentroidFold: 0.475 Positive Predictive Value ContextFold: 0.746 CentroidFold: 0.600 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.860 RNASampler(20): 0.676 Sensitivity ContextFold: 0.827 RNASampler(20): 0.522 Positive Predictive Value ContextFold: 0.895 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.686 Contrafold: 0.521 Sensitivity ContextFold: 0.648 Contrafold: 0.506 Positive Predictive Value ContextFold: 0.725 Contrafold: 0.537 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.686 Sfold: 0.481 Sensitivity ContextFold: 0.648 Sfold: 0.433 Positive Predictive Value ContextFold: 0.725 Sfold: 0.535 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs ContextFold Matthews Correlation Coefficient Multilign(seed): 0.681 ContextFold: 0.612 Sensitivity Multilign(seed): 0.649 ContextFold: 0.592 Positive Predictive Value Multilign(seed): 0.717 ContextFold: 0.633 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.686 MaxExpect: 0.476 Sensitivity ContextFold: 0.648 MaxExpect: 0.465 Positive Predictive Value ContextFold: 0.725 MaxExpect: 0.488 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.686 ProbKnot: 0.471 Sensitivity ContextFold: 0.648 ProbKnot: 0.468 Positive Predictive Value ContextFold: 0.725 ProbKnot: 0.475 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.686 Fold: 0.448 Sensitivity ContextFold: 0.648 Fold: 0.453 Positive Predictive Value ContextFold: 0.725 Fold: 0.444 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.692 RNASampler(seed): 0.629 Sensitivity ContextFold: 0.649 RNASampler(seed): 0.468 Positive Predictive Value ContextFold: 0.740 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.680 UNAFold: 0.445 Sensitivity ContextFold: 0.644 UNAFold: 0.445 Positive Predictive Value ContextFold: 0.718 UNAFold: 0.446 Number of pairs reference - predicted secondary structure: 1987 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.749 RNAsubopt: 0.525 Sensitivity ContextFold: 0.712 RNAsubopt: 0.530 Positive Predictive Value ContextFold: 0.789 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.791 RSpredict(20): 0.487 Sensitivity ContextFold: 0.752 RSpredict(20): 0.402 Positive Predictive Value ContextFold: 0.832 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.863 CMfinder(20): 0.549 Sensitivity ContextFold: 0.823 CMfinder(20): 0.380 Positive Predictive Value ContextFold: 0.906 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.735 PknotsRG: 0.466 Sensitivity ContextFold: 0.697 PknotsRG: 0.467 Positive Predictive Value ContextFold: 0.776 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.791 Carnac(20): 0.518 Sensitivity ContextFold: 0.752 Carnac(20): 0.301 Positive Predictive Value ContextFold: 0.832 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.686 RNAfold: 0.440 Sensitivity ContextFold: 0.648 RNAfold: 0.443 Positive Predictive Value ContextFold: 0.725 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.774 CMfinder(seed): 0.486 Sensitivity ContextFold: 0.739 CMfinder(seed): 0.312 Positive Predictive Value ContextFold: 0.812 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.691 Afold: 0.434 Sensitivity ContextFold: 0.653 Afold: 0.433 Positive Predictive Value ContextFold: 0.733 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.778 HotKnots: 0.613 Sensitivity ContextFold: 0.740 HotKnots: 0.607 Positive Predictive Value ContextFold: 0.822 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.729 CRWrnafold: 0.437 Sensitivity ContextFold: 0.691 CRWrnafold: 0.440 Positive Predictive Value ContextFold: 0.770 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.763 Pknots: 0.606 Sensitivity ContextFold: 0.721 Pknots: 0.595 Positive Predictive Value ContextFold: 0.811 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.730 McQFold: 0.467 Sensitivity ContextFold: 0.696 McQFold: 0.457 Positive Predictive Value ContextFold: 0.768 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.753 RNAshapes: 0.477 Sensitivity ContextFold: 0.715 RNAshapes: 0.472 Positive Predictive Value ContextFold: 0.794 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.773 PPfold(seed): 0.626 Sensitivity ContextFold: 0.755 PPfold(seed): 0.495 Positive Predictive Value ContextFold: 0.793 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.748 Mastr(20): 0.296 Sensitivity ContextFold: 0.712 Mastr(20): 0.111 Positive Predictive Value ContextFold: 0.787 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.761 Murlet(seed): 0.540 Sensitivity ContextFold: 0.727 Murlet(seed): 0.360 Positive Predictive Value ContextFold: 0.798 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.755 RNASLOpt: 0.470 Sensitivity ContextFold: 0.717 RNASLOpt: 0.442 Positive Predictive Value ContextFold: 0.795 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.805 Cylofold: 0.575 Sensitivity ContextFold: 0.765 Cylofold: 0.551 Positive Predictive Value ContextFold: 0.851 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.724 RNAwolf: 0.343 Sensitivity ContextFold: 0.687 RNAwolf: 0.358 Positive Predictive Value ContextFold: 0.763 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.751 Vsfold4: 0.346 Sensitivity ContextFold: 0.713 Vsfold4: 0.318 Positive Predictive Value ContextFold: 0.791 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.752 Vsfold5: 0.339 Sensitivity ContextFold: 0.715 Vsfold5: 0.322 Positive Predictive Value ContextFold: 0.793 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.765 Alterna: 0.552 Sensitivity ContextFold: 0.723 Alterna: 0.547 Positive Predictive Value ContextFold: 0.814 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.765 RDfolder: 0.520 Sensitivity ContextFold: 0.723 RDfolder: 0.464 Positive Predictive Value ContextFold: 0.814 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.735 Carnac(seed): 0.244 Sensitivity ContextFold: 0.710 Carnac(seed): 0.069 Positive Predictive Value ContextFold: 0.762 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.771 MCFold: 0.473 Sensitivity ContextFold: 0.731 MCFold: 0.524 Positive Predictive Value ContextFold: 0.817 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.811 RSpredict(seed): 0.369 Sensitivity ContextFold: 0.772 RSpredict(seed): 0.229 Positive Predictive Value ContextFold: 0.851 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.788 NanoFolder: 0.194 Sensitivity ContextFold: 0.749 NanoFolder: 0.229 Positive Predictive Value ContextFold: 0.831 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.796 Mastr(seed): 0.113 Sensitivity ContextFold: 0.762 Mastr(seed): 0.016 Positive Predictive Value ContextFold: 0.831 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08
TurboFold(20)	19 TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.864 TurboFold(seed): 0.858 Sensitivity TurboFold(20): 0.857 TurboFold(seed): 0.851 Positive Predictive Value TurboFold(20): 0.873 TurboFold(seed): 0.867 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 4.42992852122e-09	549 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.800 TurboFold(20): 0.788 Sensitivity PETfold_pre2.0(seed): 0.728 TurboFold(20): 0.739 Positive Predictive Value PETfold_pre2.0(seed): 0.878 TurboFold(20): 0.841 Number of pairs reference - predicted secondary structure: 549 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.863 TurboFold(20): 0.787 Sensitivity ContextFold: 0.823 TurboFold(20): 0.740 Positive Predictive Value ContextFold: 0.906 TurboFold(20): 0.837 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.779 CentroidAlifold(seed): 0.745 Sensitivity TurboFold(20): 0.731 CentroidAlifold(seed): 0.588 Positive Predictive Value TurboFold(20): 0.831 CentroidAlifold(seed): 0.943 Number of pairs reference - predicted secondary structure: 344 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.787 PETfold_pre2.0(20): 0.766 Sensitivity TurboFold(20): 0.740 PETfold_pre2.0(20): 0.675 Positive Predictive Value TurboFold(20): 0.839 PETfold_pre2.0(20): 0.870 Number of pairs reference - predicted secondary structure: 562 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(20): 0.787 CentroidAlifold(20): 0.757 Sensitivity TurboFold(20): 0.740 CentroidAlifold(20): 0.618 Positive Predictive Value TurboFold(20): 0.837 CentroidAlifold(20): 0.928 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.787 CentroidHomfold‑LAST: 0.749 Sensitivity TurboFold(20): 0.740 CentroidHomfold‑LAST: 0.625 Positive Predictive Value TurboFold(20): 0.837 CentroidHomfold‑LAST: 0.899 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.787 PPfold(20): 0.759 Sensitivity TurboFold(20): 0.740 PPfold(20): 0.652 Positive Predictive Value TurboFold(20): 0.838 PPfold(20): 0.885 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.787 RNAalifold(20): 0.705 Sensitivity TurboFold(20): 0.740 RNAalifold(20): 0.577 Positive Predictive Value TurboFold(20): 0.837 RNAalifold(20): 0.863 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.781 MXScarna(seed): 0.701 Sensitivity TurboFold(20): 0.733 MXScarna(seed): 0.607 Positive Predictive Value TurboFold(20): 0.833 MXScarna(seed): 0.810 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.787 MXScarna(20): 0.701 Sensitivity TurboFold(20): 0.740 MXScarna(20): 0.634 Positive Predictive Value TurboFold(20): 0.837 MXScarna(20): 0.776 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.787 IPknot: 0.688 Sensitivity TurboFold(20): 0.740 IPknot: 0.629 Positive Predictive Value TurboFold(20): 0.837 IPknot: 0.753 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.786 Multilign(20): 0.685 Sensitivity TurboFold(20): 0.739 Multilign(20): 0.617 Positive Predictive Value TurboFold(20): 0.837 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.793 Murlet(20): 0.631 Sensitivity TurboFold(20): 0.747 Murlet(20): 0.496 Positive Predictive Value TurboFold(20): 0.842 Murlet(20): 0.803 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.779 RNAalifold(seed): 0.508 Sensitivity TurboFold(20): 0.731 RNAalifold(seed): 0.302 Positive Predictive Value TurboFold(20): 0.831 RNAalifold(seed): 0.854 Number of pairs reference - predicted secondary structure: 340 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.787 CentroidFold: 0.650 Sensitivity TurboFold(20): 0.740 CentroidFold: 0.595 Positive Predictive Value TurboFold(20): 0.837 CentroidFold: 0.713 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.816 RNASampler(20): 0.676 Sensitivity TurboFold(20): 0.780 RNASampler(20): 0.522 Positive Predictive Value TurboFold(20): 0.856 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.787 Contrafold: 0.638 Sensitivity TurboFold(20): 0.740 Contrafold: 0.620 Positive Predictive Value TurboFold(20): 0.837 Contrafold: 0.658 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.787 Sfold: 0.613 Sensitivity TurboFold(20): 0.740 Sfold: 0.556 Positive Predictive Value TurboFold(20): 0.837 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): 0.571 Multilign(seed): 0.334 Sensitivity TurboFold(20): 0.512 Multilign(seed): 0.186 Positive Predictive Value TurboFold(20): 0.647 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.787 MaxExpect: 0.622 Sensitivity TurboFold(20): 0.740 MaxExpect: 0.602 Positive Predictive Value TurboFold(20): 0.837 MaxExpect: 0.644 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.787 ProbKnot: 0.619 Sensitivity TurboFold(20): 0.740 ProbKnot: 0.604 Positive Predictive Value TurboFold(20): 0.837 ProbKnot: 0.637 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.787 Fold: 0.599 Sensitivity TurboFold(20): 0.740 Fold: 0.593 Positive Predictive Value TurboFold(20): 0.837 Fold: 0.607 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.769 RNASampler(seed): 0.571 Sensitivity TurboFold(20): 0.707 RNASampler(seed): 0.343 Positive Predictive Value TurboFold(20): 0.841 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.787 UNAFold: 0.587 Sensitivity TurboFold(20): 0.740 UNAFold: 0.575 Positive Predictive Value TurboFold(20): 0.837 UNAFold: 0.600 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.787 RNAsubopt: 0.570 Sensitivity TurboFold(20): 0.740 RNAsubopt: 0.570 Positive Predictive Value TurboFold(20): 0.837 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.787 RSpredict(20): 0.524 Sensitivity TurboFold(20): 0.740 RSpredict(20): 0.385 Positive Predictive Value TurboFold(20): 0.837 RSpredict(20): 0.714 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.786 CMfinder(20): 0.549 Sensitivity TurboFold(20): 0.740 CMfinder(20): 0.380 Positive Predictive Value TurboFold(20): 0.837 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.787 PknotsRG: 0.566 Sensitivity TurboFold(20): 0.740 PknotsRG: 0.559 Positive Predictive Value TurboFold(20): 0.837 PknotsRG: 0.575 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.787 Carnac(20): 0.469 Sensitivity TurboFold(20): 0.740 Carnac(20): 0.248 Positive Predictive Value TurboFold(20): 0.837 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.787 RNAfold: 0.579 Sensitivity TurboFold(20): 0.740 RNAfold: 0.572 Positive Predictive Value TurboFold(20): 0.837 RNAfold: 0.588 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): 0.744 CMfinder(seed): 0.736 Sensitivity TurboFold(20): 0.678 CMfinder(seed): 0.607 Positive Predictive Value TurboFold(20): 0.821 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 1.15003019969e-05	+ TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.780 Afold: 0.572 Sensitivity TurboFold(20): 0.730 Afold: 0.560 Positive Predictive Value TurboFold(20): 0.834 Afold: 0.586 Number of pairs reference - predicted secondary structure: 348 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.889 HotKnots: 0.698 Sensitivity TurboFold(20): 0.861 HotKnots: 0.695 Positive Predictive Value TurboFold(20): 0.919 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.787 CRWrnafold: 0.542 Sensitivity TurboFold(20): 0.740 CRWrnafold: 0.533 Positive Predictive Value TurboFold(20): 0.837 CRWrnafold: 0.553 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.910 Pknots: 0.655 Sensitivity TurboFold(20): 0.885 Pknots: 0.662 Positive Predictive Value TurboFold(20): 0.937 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.787 McQFold: 0.484 Sensitivity TurboFold(20): 0.740 McQFold: 0.464 Positive Predictive Value TurboFold(20): 0.837 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.787 RNAshapes: 0.526 Sensitivity TurboFold(20): 0.741 RNAshapes: 0.514 Positive Predictive Value TurboFold(20): 0.838 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.872 PPfold(seed): 0.453 Sensitivity TurboFold(20): 0.866 PPfold(seed): 0.224 Positive Predictive Value TurboFold(20): 0.880 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.787 Mastr(20): 0.350 Sensitivity TurboFold(20): 0.740 Mastr(20): 0.156 Positive Predictive Value TurboFold(20): 0.837 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.802 Murlet(seed): 0.631 Sensitivity TurboFold(20): 0.747 Murlet(seed): 0.418 Positive Predictive Value TurboFold(20): 0.864 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.787 RNASLOpt: 0.500 Sensitivity TurboFold(20): 0.742 RNASLOpt: 0.464 Positive Predictive Value TurboFold(20): 0.837 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.892 Cylofold: 0.557 Sensitivity TurboFold(20): 0.864 Cylofold: 0.543 Positive Predictive Value TurboFold(20): 0.922 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.787 RNAwolf: 0.414 Sensitivity TurboFold(20): 0.740 RNAwolf: 0.423 Positive Predictive Value TurboFold(20): 0.837 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.787 Vsfold4: 0.390 Sensitivity TurboFold(20): 0.740 Vsfold4: 0.356 Positive Predictive Value TurboFold(20): 0.837 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.787 Vsfold5: 0.365 Sensitivity TurboFold(20): 0.740 Vsfold5: 0.341 Positive Predictive Value TurboFold(20): 0.837 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.913 Alterna: 0.618 Sensitivity TurboFold(20): 0.887 Alterna: 0.626 Positive Predictive Value TurboFold(20): 0.940 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.913 RDfolder: 0.556 Sensitivity TurboFold(20): 0.887 RDfolder: 0.511 Positive Predictive Value TurboFold(20): 0.940 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.843 Carnac(seed): 0.310 Sensitivity TurboFold(20): 0.811 Carnac(seed): 0.106 Positive Predictive Value TurboFold(20): 0.877 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.885 MCFold: 0.500 Sensitivity TurboFold(20): 0.859 MCFold: 0.559 Positive Predictive Value TurboFold(20): 0.914 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.779 RSpredict(seed): 0.238 Sensitivity TurboFold(20): 0.731 RSpredict(seed): 0.104 Positive Predictive Value TurboFold(20): 0.831 RSpredict(seed): 0.546 Number of pairs reference - predicted secondary structure: 346 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.768 NanoFolder: 0.189 Sensitivity TurboFold(20): 0.720 NanoFolder: 0.218 Positive Predictive Value TurboFold(20): 0.820 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.783 Mastr(seed): 0.106 Sensitivity TurboFold(20): 0.736 Mastr(seed): 0.014 Positive Predictive Value TurboFold(20): 0.834 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 343 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(seed)	50 TurboFold(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.788 CentroidAlifold(seed): 0.767 Sensitivity TurboFold(seed): 0.760 CentroidAlifold(seed): 0.675 Positive Predictive Value TurboFold(seed): 0.819 CentroidAlifold(seed): 0.872 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 7.04732813174e-08	688 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.764 CentroidAlifold(seed): 0.752 Sensitivity PETfold_pre2.0(seed): 0.701 CentroidAlifold(seed): 0.628 Positive Predictive Value PETfold_pre2.0(seed): 0.834 CentroidAlifold(seed): 0.901 Number of pairs reference - predicted secondary structure: 688 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.812 CentroidAlifold(seed): 0.749 Sensitivity ContextFold: 0.774 CentroidAlifold(seed): 0.623 Positive Predictive Value ContextFold: 0.853 CentroidAlifold(seed): 0.901 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	344 TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.779 CentroidAlifold(seed): 0.745 Sensitivity TurboFold(20): 0.731 CentroidAlifold(seed): 0.588 Positive Predictive Value TurboFold(20): 0.831 CentroidAlifold(seed): 0.943 Number of pairs reference - predicted secondary structure: 344 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidAlifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.775 PETfold_pre2.0(20): 0.765 Sensitivity CentroidAlifold(seed): 0.653 PETfold_pre2.0(20): 0.702 Positive Predictive Value CentroidAlifold(seed): 0.918 PETfold_pre2.0(20): 0.834 Number of pairs reference - predicted secondary structure: 399 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 CentroidAlifold(20): 0.761 Sensitivity CentroidAlifold(seed): 0.652 CentroidAlifold(20): 0.638 Positive Predictive Value CentroidAlifold(seed): 0.918 CentroidAlifold(20): 0.909 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 CentroidHomfold‑LAST: 0.699 Sensitivity CentroidAlifold(seed): 0.577 CentroidHomfold‑LAST: 0.561 Positive Predictive Value CentroidAlifold(seed): 0.905 CentroidHomfold‑LAST: 0.872 Number of pairs reference - predicted secondary structure: 629 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.753 PPfold(20): 0.739 Sensitivity CentroidAlifold(seed): 0.603 PPfold(20): 0.627 Positive Predictive Value CentroidAlifold(seed): 0.942 PPfold(20): 0.873 Number of pairs reference - predicted secondary structure: 335 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 RNAalifold(20): 0.716 Sensitivity CentroidAlifold(seed): 0.652 RNAalifold(20): 0.621 Positive Predictive Value CentroidAlifold(seed): 0.918 RNAalifold(20): 0.825 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 MXScarna(seed): 0.653 Sensitivity CentroidAlifold(seed): 0.623 MXScarna(seed): 0.567 Positive Predictive Value CentroidAlifold(seed): 0.901 MXScarna(seed): 0.752 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 MXScarna(20): 0.668 Sensitivity CentroidAlifold(seed): 0.652 MXScarna(20): 0.600 Positive Predictive Value CentroidAlifold(seed): 0.918 MXScarna(20): 0.744 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 IPknot: 0.632 Sensitivity CentroidAlifold(seed): 0.623 IPknot: 0.570 Positive Predictive Value CentroidAlifold(seed): 0.901 IPknot: 0.702 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.740 Multilign(20): 0.650 Sensitivity CentroidAlifold(seed): 0.580 Multilign(20): 0.573 Positive Predictive Value CentroidAlifold(seed): 0.945 Multilign(20): 0.738 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.763 Murlet(20): 0.589 Sensitivity CentroidAlifold(seed): 0.627 Murlet(20): 0.450 Positive Predictive Value CentroidAlifold(seed): 0.930 Murlet(20): 0.770 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.750 RNAalifold(seed): 0.640 Sensitivity CentroidAlifold(seed): 0.624 RNAalifold(seed): 0.486 Positive Predictive Value CentroidAlifold(seed): 0.901 RNAalifold(seed): 0.844 Number of pairs reference - predicted secondary structure: 695 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.751 CentroidFold: 0.598 Sensitivity CentroidAlifold(seed): 0.626 CentroidFold: 0.538 Positive Predictive Value CentroidAlifold(seed): 0.902 CentroidFold: 0.667 Number of pairs reference - predicted secondary structure: 705 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.792 RNASampler(20): 0.590 Sensitivity CentroidAlifold(seed): 0.674 RNASampler(20): 0.389 Positive Predictive Value CentroidAlifold(seed): 0.931 RNASampler(20): 0.898 Number of pairs reference - predicted secondary structure: 178 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 Contrafold: 0.584 Sensitivity CentroidAlifold(seed): 0.623 Contrafold: 0.565 Positive Predictive Value CentroidAlifold(seed): 0.901 Contrafold: 0.604 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 Sfold: 0.570 Sensitivity CentroidAlifold(seed): 0.623 Sfold: 0.514 Positive Predictive Value CentroidAlifold(seed): 0.901 Sfold: 0.632 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.777 Multilign(seed): 0.698 Sensitivity CentroidAlifold(seed): 0.703 Multilign(seed): 0.660 Positive Predictive Value CentroidAlifold(seed): 0.859 Multilign(seed): 0.741 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 MaxExpect: 0.544 Sensitivity CentroidAlifold(seed): 0.623 MaxExpect: 0.529 Positive Predictive Value CentroidAlifold(seed): 0.901 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 ProbKnot: 0.540 Sensitivity CentroidAlifold(seed): 0.623 ProbKnot: 0.529 Positive Predictive Value CentroidAlifold(seed): 0.901 ProbKnot: 0.551 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 Fold: 0.519 Sensitivity CentroidAlifold(seed): 0.623 Fold: 0.518 Positive Predictive Value CentroidAlifold(seed): 0.901 Fold: 0.521 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.852 RNASampler(seed): 0.629 Sensitivity CentroidAlifold(seed): 0.740 RNASampler(seed): 0.468 Positive Predictive Value CentroidAlifold(seed): 0.983 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 UNAFold: 0.536 Sensitivity CentroidAlifold(seed): 0.623 UNAFold: 0.528 Positive Predictive Value CentroidAlifold(seed): 0.901 UNAFold: 0.546 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 RNAsubopt: 0.570 Sensitivity CentroidAlifold(seed): 0.577 RNAsubopt: 0.571 Positive Predictive Value CentroidAlifold(seed): 0.905 RNAsubopt: 0.570 Number of pairs reference - predicted secondary structure: 629 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 RSpredict(20): 0.532 Sensitivity CentroidAlifold(seed): 0.652 RSpredict(20): 0.425 Positive Predictive Value CentroidAlifold(seed): 0.918 RSpredict(20): 0.666 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.744 CMfinder(20): 0.519 Sensitivity CentroidAlifold(seed): 0.588 CMfinder(20): 0.350 Positive Predictive Value CentroidAlifold(seed): 0.943 CMfinder(20): 0.773 Number of pairs reference - predicted secondary structure: 340 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.762 PknotsRG: 0.529 Sensitivity CentroidAlifold(seed): 0.640 PknotsRG: 0.523 Positive Predictive Value CentroidAlifold(seed): 0.908 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 694 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 Carnac(20): 0.506 Sensitivity CentroidAlifold(seed): 0.652 Carnac(20): 0.283 Positive Predictive Value CentroidAlifold(seed): 0.918 Carnac(20): 0.903 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 RNAfold: 0.520 Sensitivity CentroidAlifold(seed): 0.623 RNAfold: 0.515 Positive Predictive Value CentroidAlifold(seed): 0.901 RNAfold: 0.526 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.766 CMfinder(seed): 0.486 Sensitivity CentroidAlifold(seed): 0.635 CMfinder(seed): 0.312 Positive Predictive Value CentroidAlifold(seed): 0.925 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.751 Afold: 0.515 Sensitivity CentroidAlifold(seed): 0.625 Afold: 0.508 Positive Predictive Value CentroidAlifold(seed): 0.903 Afold: 0.522 Number of pairs reference - predicted secondary structure: 576 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.789 HotKnots: 0.687 Sensitivity CentroidAlifold(seed): 0.698 HotKnots: 0.688 Positive Predictive Value CentroidAlifold(seed): 0.895 HotKnots: 0.691 Number of pairs reference - predicted secondary structure: 213 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.748 CRWrnafold: 0.508 Sensitivity CentroidAlifold(seed): 0.618 CRWrnafold: 0.503 Positive Predictive Value CentroidAlifold(seed): 0.905 CRWrnafold: 0.514 Number of pairs reference - predicted secondary structure: 671 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.780 Pknots: 0.509 Sensitivity CentroidAlifold(seed): 0.673 Pknots: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.906 Pknots: 0.523 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.719 McQFold: 0.475 Sensitivity CentroidAlifold(seed): 0.571 McQFold: 0.458 Positive Predictive Value CentroidAlifold(seed): 0.905 McQFold: 0.495 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.726 RNAshapes: 0.528 Sensitivity CentroidAlifold(seed): 0.583 RNAshapes: 0.517 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 604 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 PPfold(seed): 0.626 Sensitivity CentroidAlifold(seed): 0.646 PPfold(seed): 0.495 Positive Predictive Value CentroidAlifold(seed): 0.832 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.716 Mastr(20): 0.224 Sensitivity CentroidAlifold(seed): 0.558 Mastr(20): 0.061 Positive Predictive Value CentroidAlifold(seed): 0.921 Mastr(20): 0.827 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.817 Murlet(seed): 0.540 Sensitivity CentroidAlifold(seed): 0.728 Murlet(seed): 0.360 Positive Predictive Value CentroidAlifold(seed): 0.916 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.736 RNASLOpt: 0.479 Sensitivity CentroidAlifold(seed): 0.596 RNASLOpt: 0.446 Positive Predictive Value CentroidAlifold(seed): 0.910 RNASLOpt: 0.517 Number of pairs reference - predicted secondary structure: 581 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.785 Cylofold: 0.518 Sensitivity CentroidAlifold(seed): 0.694 Cylofold: 0.491 Positive Predictive Value CentroidAlifold(seed): 0.892 Cylofold: 0.552 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.719 RNAwolf: 0.395 Sensitivity CentroidAlifold(seed): 0.571 RNAwolf: 0.404 Positive Predictive Value CentroidAlifold(seed): 0.905 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.726 Vsfold4: 0.338 Sensitivity CentroidAlifold(seed): 0.583 Vsfold4: 0.307 Positive Predictive Value CentroidAlifold(seed): 0.905 Vsfold4: 0.375 Number of pairs reference - predicted secondary structure: 614 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.727 Vsfold5: 0.314 Sensitivity CentroidAlifold(seed): 0.584 Vsfold5: 0.293 Positive Predictive Value CentroidAlifold(seed): 0.905 Vsfold5: 0.339 Number of pairs reference - predicted secondary structure: 609 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.781 Alterna: 0.558 Sensitivity CentroidAlifold(seed): 0.674 Alterna: 0.548 Positive Predictive Value CentroidAlifold(seed): 0.908 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.781 RDfolder: 0.468 Sensitivity CentroidAlifold(seed): 0.674 RDfolder: 0.402 Positive Predictive Value CentroidAlifold(seed): 0.908 RDfolder: 0.552 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 Carnac(seed): 0.245 Sensitivity CentroidAlifold(seed): 0.599 Carnac(seed): 0.069 Positive Predictive Value CentroidAlifold(seed): 0.885 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 266 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.786 MCFold: 0.472 Sensitivity CentroidAlifold(seed): 0.691 MCFold: 0.523 Positive Predictive Value CentroidAlifold(seed): 0.896 MCFold: 0.432 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.748 RSpredict(seed): 0.370 Sensitivity CentroidAlifold(seed): 0.620 RSpredict(seed): 0.230 Positive Predictive Value CentroidAlifold(seed): 0.902 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 699 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.732 NanoFolder: 0.201 Sensitivity CentroidAlifold(seed): 0.580 NanoFolder: 0.231 Positive Predictive Value CentroidAlifold(seed): 0.925 NanoFolder: 0.178 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.714 Mastr(seed): 0.114 Sensitivity CentroidAlifold(seed): 0.568 Mastr(seed): 0.016 Positive Predictive Value CentroidAlifold(seed): 0.899 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 618 Wilcoxon single-rank test P-value: 3.56938820447e-08
PETfold_pre2.0(20)	19 TurboFold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 PETfold_pre2.0(20): 0.605 Sensitivity TurboFold(seed): 0.851 PETfold_pre2.0(20): 0.395 Positive Predictive Value TurboFold(seed): 0.867 PETfold_pre2.0(20): 0.929 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 4.00488379386e-09	626 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 PETfold_pre2.0(20): 0.747 Sensitivity PETfold_pre2.0(seed): 0.729 PETfold_pre2.0(20): 0.692 Positive Predictive Value PETfold_pre2.0(seed): 0.830 PETfold_pre2.0(20): 0.807 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 ContextFold vs PETfold_pre2.0(20) Matthews Correlation Coefficient ContextFold: 0.791 PETfold_pre2.0(20): 0.744 Sensitivity ContextFold: 0.752 PETfold_pre2.0(20): 0.686 Positive Predictive Value ContextFold: 0.832 PETfold_pre2.0(20): 0.807 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	562 TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.787 PETfold_pre2.0(20): 0.766 Sensitivity TurboFold(20): 0.740 PETfold_pre2.0(20): 0.675 Positive Predictive Value TurboFold(20): 0.839 PETfold_pre2.0(20): 0.870 Number of pairs reference - predicted secondary structure: 562 Wilcoxon single-rank test P-value: 3.56938820447e-08	399 CentroidAlifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.775 PETfold_pre2.0(20): 0.765 Sensitivity CentroidAlifold(seed): 0.653 PETfold_pre2.0(20): 0.702 Positive Predictive Value CentroidAlifold(seed): 0.918 PETfold_pre2.0(20): 0.834 Number of pairs reference - predicted secondary structure: 399 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ PETfold_pre2.0(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 CentroidAlifold(20): 0.741 Sensitivity PETfold_pre2.0(20): 0.686 CentroidAlifold(20): 0.616 Positive Predictive Value PETfold_pre2.0(20): 0.807 CentroidAlifold(20): 0.891 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 CentroidHomfold‑LAST: 0.750 Sensitivity PETfold_pre2.0(20): 0.675 CentroidHomfold‑LAST: 0.626 Positive Predictive Value PETfold_pre2.0(20): 0.870 CentroidHomfold‑LAST: 0.899 Number of pairs reference - predicted secondary structure: 562 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 PPfold(20): 0.760 Sensitivity PETfold_pre2.0(20): 0.681 PPfold(20): 0.657 Positive Predictive Value PETfold_pre2.0(20): 0.862 PPfold(20): 0.879 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 RNAalifold(20): 0.687 Sensitivity PETfold_pre2.0(20): 0.686 RNAalifold(20): 0.601 Positive Predictive Value PETfold_pre2.0(20): 0.807 RNAalifold(20): 0.787 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 MXScarna(seed): 0.682 Sensitivity PETfold_pre2.0(20): 0.703 MXScarna(seed): 0.601 Positive Predictive Value PETfold_pre2.0(20): 0.835 MXScarna(seed): 0.774 Number of pairs reference - predicted secondary structure: 413 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 MXScarna(20): 0.646 Sensitivity PETfold_pre2.0(20): 0.686 MXScarna(20): 0.589 Positive Predictive Value PETfold_pre2.0(20): 0.807 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 IPknot: 0.608 Sensitivity PETfold_pre2.0(20): 0.686 IPknot: 0.545 Positive Predictive Value PETfold_pre2.0(20): 0.807 IPknot: 0.679 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.768 Multilign(20): 0.685 Sensitivity PETfold_pre2.0(20): 0.677 Multilign(20): 0.618 Positive Predictive Value PETfold_pre2.0(20): 0.871 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 531 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 Murlet(20): 0.629 Sensitivity PETfold_pre2.0(20): 0.686 Murlet(20): 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.855 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.757 RNAalifold(seed): 0.648 Sensitivity PETfold_pre2.0(20): 0.695 RNAalifold(seed): 0.508 Positive Predictive Value PETfold_pre2.0(20): 0.825 RNAalifold(seed): 0.826 Number of pairs reference - predicted secondary structure: 399 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.746 CentroidFold: 0.569 Sensitivity PETfold_pre2.0(20): 0.688 CentroidFold: 0.508 Positive Predictive Value PETfold_pre2.0(20): 0.809 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 638 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.779 RNASampler(20): 0.677 Sensitivity PETfold_pre2.0(20): 0.680 RNASampler(20): 0.524 Positive Predictive Value PETfold_pre2.0(20): 0.894 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 391 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 Contrafold: 0.553 Sensitivity PETfold_pre2.0(20): 0.686 Contrafold: 0.536 Positive Predictive Value PETfold_pre2.0(20): 0.807 Contrafold: 0.572 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 Sfold: 0.529 Sensitivity PETfold_pre2.0(20): 0.686 Sfold: 0.475 Positive Predictive Value PETfold_pre2.0(20): 0.807 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.473 Multilign(seed): 0.334 Sensitivity PETfold_pre2.0(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value PETfold_pre2.0(20): 0.700 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 MaxExpect: 0.512 Sensitivity PETfold_pre2.0(20): 0.686 MaxExpect: 0.498 Positive Predictive Value PETfold_pre2.0(20): 0.807 MaxExpect: 0.526 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 ProbKnot: 0.507 Sensitivity PETfold_pre2.0(20): 0.686 ProbKnot: 0.497 Positive Predictive Value PETfold_pre2.0(20): 0.807 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 Fold: 0.485 Sensitivity PETfold_pre2.0(20): 0.686 Fold: 0.485 Positive Predictive Value PETfold_pre2.0(20): 0.807 Fold: 0.485 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNASampler(seed): 0.571 Sensitivity PETfold_pre2.0(20): 0.627 RNASampler(seed): 0.343 Positive Predictive Value PETfold_pre2.0(20): 0.867 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 UNAFold: 0.496 Sensitivity PETfold_pre2.0(20): 0.686 UNAFold: 0.490 Positive Predictive Value PETfold_pre2.0(20): 0.807 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 RNAsubopt: 0.571 Sensitivity PETfold_pre2.0(20): 0.675 RNAsubopt: 0.570 Positive Predictive Value PETfold_pre2.0(20): 0.870 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 562 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 RSpredict(20): 0.487 Sensitivity PETfold_pre2.0(20): 0.686 RSpredict(20): 0.402 Positive Predictive Value PETfold_pre2.0(20): 0.807 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.767 CMfinder(20): 0.550 Sensitivity PETfold_pre2.0(20): 0.676 CMfinder(20): 0.381 Positive Predictive Value PETfold_pre2.0(20): 0.870 CMfinder(20): 0.795 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.792 PknotsRG: 0.521 Sensitivity PETfold_pre2.0(20): 0.728 PknotsRG: 0.514 Positive Predictive Value PETfold_pre2.0(20): 0.861 PknotsRG: 0.528 Number of pairs reference - predicted secondary structure: 608 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 Carnac(20): 0.519 Sensitivity PETfold_pre2.0(20): 0.686 Carnac(20): 0.302 Positive Predictive Value PETfold_pre2.0(20): 0.807 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 RNAfold: 0.481 Sensitivity PETfold_pre2.0(20): 0.686 RNAfold: 0.480 Positive Predictive Value PETfold_pre2.0(20): 0.807 RNAfold: 0.483 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 PETfold_pre2.0(20): 0.708 Sensitivity CMfinder(seed): 0.607 PETfold_pre2.0(20): 0.594 Positive Predictive Value CMfinder(seed): 0.898 PETfold_pre2.0(20): 0.851 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 Afold: 0.473 Sensitivity PETfold_pre2.0(20): 0.679 Afold: 0.469 Positive Predictive Value PETfold_pre2.0(20): 0.798 Afold: 0.479 Number of pairs reference - predicted secondary structure: 418 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 HotKnots: 0.698 Sensitivity PETfold_pre2.0(20): 0.737 HotKnots: 0.695 Positive Predictive Value PETfold_pre2.0(20): 0.975 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.784 CRWrnafold: 0.540 Sensitivity PETfold_pre2.0(20): 0.712 CRWrnafold: 0.531 Positive Predictive Value PETfold_pre2.0(20): 0.864 CRWrnafold: 0.550 Number of pairs reference - predicted secondary structure: 587 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.885 Pknots: 0.655 Sensitivity PETfold_pre2.0(20): 0.807 Pknots: 0.662 Positive Predictive Value PETfold_pre2.0(20): 0.972 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 McQFold: 0.484 Sensitivity PETfold_pre2.0(20): 0.675 McQFold: 0.464 Positive Predictive Value PETfold_pre2.0(20): 0.870 McQFold: 0.508 Number of pairs reference - predicted secondary structure: 562 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.768 RNAshapes: 0.526 Sensitivity PETfold_pre2.0(20): 0.677 RNAshapes: 0.513 Positive Predictive Value PETfold_pre2.0(20): 0.873 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.669 PPfold(seed): 0.453 Sensitivity PETfold_pre2.0(20): 0.473 PPfold(seed): 0.224 Positive Predictive Value PETfold_pre2.0(20): 0.948 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.69811216434e-08	+ PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.707 Mastr(20): 0.297 Sensitivity PETfold_pre2.0(20): 0.634 Mastr(20): 0.111 Positive Predictive Value PETfold_pre2.0(20): 0.788 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 589 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 Murlet(seed): 0.631 Sensitivity PETfold_pre2.0(20): 0.618 Murlet(seed): 0.418 Positive Predictive Value PETfold_pre2.0(20): 0.882 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.769 RNASLOpt: 0.500 Sensitivity PETfold_pre2.0(20): 0.679 RNASLOpt: 0.463 Positive Predictive Value PETfold_pre2.0(20): 0.872 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 544 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.845 Cylofold: 0.557 Sensitivity PETfold_pre2.0(20): 0.735 Cylofold: 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.974 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 RNAwolf: 0.414 Sensitivity PETfold_pre2.0(20): 0.675 RNAwolf: 0.423 Positive Predictive Value PETfold_pre2.0(20): 0.870 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 562 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.767 Vsfold4: 0.393 Sensitivity PETfold_pre2.0(20): 0.676 Vsfold4: 0.357 Positive Predictive Value PETfold_pre2.0(20): 0.871 Vsfold4: 0.434 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.768 Vsfold5: 0.368 Sensitivity PETfold_pre2.0(20): 0.677 Vsfold5: 0.343 Positive Predictive Value PETfold_pre2.0(20): 0.871 Vsfold5: 0.397 Number of pairs reference - predicted secondary structure: 554 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): 0.887 Alterna: 0.618 Sensitivity PETfold_pre2.0(20): 0.811 Alterna: 0.626 Positive Predictive Value PETfold_pre2.0(20): 0.973 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.887 RDfolder: 0.556 Sensitivity PETfold_pre2.0(20): 0.811 RDfolder: 0.511 Positive Predictive Value PETfold_pre2.0(20): 0.973 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.781 Carnac(seed): 0.398 Sensitivity PETfold_pre2.0(20): 0.680 Carnac(seed): 0.173 Positive Predictive Value PETfold_pre2.0(20): 0.898 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.838 MCFold: 0.500 Sensitivity PETfold_pre2.0(20): 0.724 MCFold: 0.559 Positive Predictive Value PETfold_pre2.0(20): 0.973 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.762 RSpredict(seed): 0.410 Sensitivity PETfold_pre2.0(20): 0.697 RSpredict(seed): 0.276 Positive Predictive Value PETfold_pre2.0(20): 0.834 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 395 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.743 NanoFolder: 0.191 Sensitivity PETfold_pre2.0(20): 0.646 NanoFolder: 0.221 Positive Predictive Value PETfold_pre2.0(20): 0.857 NanoFolder: 0.169 Number of pairs reference - predicted secondary structure: 114 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Mastr(seed): 0.105 Sensitivity PETfold_pre2.0(20): 0.639 Mastr(seed): 0.013 Positive Predictive Value PETfold_pre2.0(20): 0.855 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 342 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(20)	19 TurboFold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 CentroidAlifold(20): 0.693 Sensitivity TurboFold(seed): 0.851 CentroidAlifold(20): 0.520 Positive Predictive Value TurboFold(seed): 0.867 CentroidAlifold(20): 0.925 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.52609899389e-08	626 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 CentroidAlifold(20): 0.742 Sensitivity PETfold_pre2.0(seed): 0.729 CentroidAlifold(20): 0.619 Positive Predictive Value PETfold_pre2.0(seed): 0.830 CentroidAlifold(20): 0.891 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 ContextFold vs CentroidAlifold(20) Matthews Correlation Coefficient ContextFold: 0.791 CentroidAlifold(20): 0.740 Sensitivity ContextFold: 0.752 CentroidAlifold(20): 0.616 Positive Predictive Value ContextFold: 0.832 CentroidAlifold(20): 0.891 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(20): 0.787 CentroidAlifold(20): 0.757 Sensitivity TurboFold(20): 0.740 CentroidAlifold(20): 0.618 Positive Predictive Value TurboFold(20): 0.837 CentroidAlifold(20): 0.928 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 CentroidAlifold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 CentroidAlifold(20): 0.761 Sensitivity CentroidAlifold(seed): 0.652 CentroidAlifold(20): 0.638 Positive Predictive Value CentroidAlifold(seed): 0.918 CentroidAlifold(20): 0.909 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 CentroidAlifold(20): 0.741 Sensitivity PETfold_pre2.0(20): 0.686 CentroidAlifold(20): 0.616 Positive Predictive Value PETfold_pre2.0(20): 0.807 CentroidAlifold(20): 0.891 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.757 CentroidHomfold‑LAST: 0.749 Sensitivity CentroidAlifold(20): 0.618 CentroidHomfold‑LAST: 0.625 Positive Predictive Value CentroidAlifold(20): 0.928 CentroidHomfold‑LAST: 0.899 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	= PPfold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(20): 0.758 CentroidAlifold(20): 0.758 Sensitivity PPfold(20): 0.654 CentroidAlifold(20): 0.622 Positive Predictive Value PPfold(20): 0.879 CentroidAlifold(20): 0.924 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 0.00586086047676	+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.740 RNAalifold(20): 0.687 Sensitivity CentroidAlifold(20): 0.616 RNAalifold(20): 0.600 Positive Predictive Value CentroidAlifold(20): 0.891 RNAalifold(20): 0.787 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.762 MXScarna(seed): 0.682 Sensitivity CentroidAlifold(20): 0.639 MXScarna(seed): 0.601 Positive Predictive Value CentroidAlifold(20): 0.909 MXScarna(seed): 0.774 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.740 MXScarna(20): 0.647 Sensitivity CentroidAlifold(20): 0.616 MXScarna(20): 0.589 Positive Predictive Value CentroidAlifold(20): 0.891 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.740 IPknot: 0.609 Sensitivity CentroidAlifold(20): 0.616 IPknot: 0.546 Positive Predictive Value CentroidAlifold(20): 0.891 IPknot: 0.679 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.758 Multilign(20): 0.685 Sensitivity CentroidAlifold(20): 0.619 Multilign(20): 0.617 Positive Predictive Value CentroidAlifold(20): 0.929 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 Murlet(20): 0.629 Sensitivity CentroidAlifold(20): 0.638 Murlet(20): 0.503 Positive Predictive Value CentroidAlifold(20): 0.915 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.753 RNAalifold(seed): 0.648 Sensitivity CentroidAlifold(20): 0.628 RNAalifold(seed): 0.508 Positive Predictive Value CentroidAlifold(20): 0.904 RNAalifold(seed): 0.826 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.742 CentroidFold: 0.569 Sensitivity CentroidAlifold(20): 0.618 CentroidFold: 0.508 Positive Predictive Value CentroidAlifold(20): 0.892 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.790 RNASampler(20): 0.676 Sensitivity CentroidAlifold(20): 0.677 RNASampler(20): 0.522 Positive Predictive Value CentroidAlifold(20): 0.923 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 Contrafold: 0.554 Sensitivity CentroidAlifold(20): 0.616 Contrafold: 0.536 Positive Predictive Value CentroidAlifold(20): 0.891 Contrafold: 0.572 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 Sfold: 0.530 Sensitivity CentroidAlifold(20): 0.616 Sfold: 0.475 Positive Predictive Value CentroidAlifold(20): 0.891 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.693 Multilign(seed): 0.334 Sensitivity CentroidAlifold(20): 0.581 Multilign(seed): 0.186 Positive Predictive Value CentroidAlifold(20): 0.833 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.740 MaxExpect: 0.512 Sensitivity CentroidAlifold(20): 0.616 MaxExpect: 0.499 Positive Predictive Value CentroidAlifold(20): 0.891 MaxExpect: 0.527 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.740 ProbKnot: 0.507 Sensitivity CentroidAlifold(20): 0.616 ProbKnot: 0.498 Positive Predictive Value CentroidAlifold(20): 0.891 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 Fold: 0.485 Sensitivity CentroidAlifold(20): 0.616 Fold: 0.486 Positive Predictive Value CentroidAlifold(20): 0.891 Fold: 0.485 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.822 RNASampler(seed): 0.571 Sensitivity CentroidAlifold(20): 0.739 RNASampler(seed): 0.343 Positive Predictive Value CentroidAlifold(20): 0.917 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 UNAFold: 0.497 Sensitivity CentroidAlifold(20): 0.616 UNAFold: 0.491 Positive Predictive Value CentroidAlifold(20): 0.891 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.757 RNAsubopt: 0.570 Sensitivity CentroidAlifold(20): 0.618 RNAsubopt: 0.570 Positive Predictive Value CentroidAlifold(20): 0.928 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.740 RSpredict(20): 0.487 Sensitivity CentroidAlifold(20): 0.616 RSpredict(20): 0.402 Positive Predictive Value CentroidAlifold(20): 0.891 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.758 CMfinder(20): 0.549 Sensitivity CentroidAlifold(20): 0.620 CMfinder(20): 0.380 Positive Predictive Value CentroidAlifold(20): 0.928 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.791 PknotsRG: 0.521 Sensitivity CentroidAlifold(20): 0.678 PknotsRG: 0.514 Positive Predictive Value CentroidAlifold(20): 0.923 PknotsRG: 0.529 Number of pairs reference - predicted secondary structure: 611 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.740 Carnac(20): 0.518 Sensitivity CentroidAlifold(20): 0.616 Carnac(20): 0.301 Positive Predictive Value CentroidAlifold(20): 0.891 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 RNAfold: 0.482 Sensitivity CentroidAlifold(20): 0.616 RNAfold: 0.480 Positive Predictive Value CentroidAlifold(20): 0.891 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.805 CMfinder(seed): 0.736 Sensitivity CentroidAlifold(20): 0.718 CMfinder(seed): 0.607 Positive Predictive Value CentroidAlifold(20): 0.907 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.731 Afold: 0.474 Sensitivity CentroidAlifold(20): 0.603 Afold: 0.470 Positive Predictive Value CentroidAlifold(20): 0.885 Afold: 0.479 Number of pairs reference - predicted secondary structure: 421 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.849 HotKnots: 0.698 Sensitivity CentroidAlifold(20): 0.754 HotKnots: 0.695 Positive Predictive Value CentroidAlifold(20): 0.957 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.779 CRWrnafold: 0.541 Sensitivity CentroidAlifold(20): 0.658 CRWrnafold: 0.532 Positive Predictive Value CentroidAlifold(20): 0.923 CRWrnafold: 0.551 Number of pairs reference - predicted secondary structure: 590 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.906 Pknots: 0.655 Sensitivity CentroidAlifold(20): 0.843 Pknots: 0.662 Positive Predictive Value CentroidAlifold(20): 0.974 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.757 McQFold: 0.484 Sensitivity CentroidAlifold(20): 0.618 McQFold: 0.464 Positive Predictive Value CentroidAlifold(20): 0.928 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.759 RNAshapes: 0.526 Sensitivity CentroidAlifold(20): 0.620 RNAshapes: 0.514 Positive Predictive Value CentroidAlifold(20): 0.929 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.736 PPfold(seed): 0.453 Sensitivity CentroidAlifold(20): 0.576 PPfold(seed): 0.224 Positive Predictive Value CentroidAlifold(20): 0.943 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.694 Mastr(20): 0.296 Sensitivity CentroidAlifold(20): 0.550 Mastr(20): 0.111 Positive Predictive Value CentroidAlifold(20): 0.877 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.804 Murlet(seed): 0.631 Sensitivity CentroidAlifold(20): 0.703 Murlet(seed): 0.418 Positive Predictive Value CentroidAlifold(20): 0.923 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.760 RNASLOpt: 0.500 Sensitivity CentroidAlifold(20): 0.624 RNASLOpt: 0.464 Positive Predictive Value CentroidAlifold(20): 0.928 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Cylofold: 0.557 Sensitivity CentroidAlifold(20): 0.753 Cylofold: 0.543 Positive Predictive Value CentroidAlifold(20): 0.959 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.757 RNAwolf: 0.414 Sensitivity CentroidAlifold(20): 0.618 RNAwolf: 0.423 Positive Predictive Value CentroidAlifold(20): 0.928 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.758 Vsfold4: 0.390 Sensitivity CentroidAlifold(20): 0.620 Vsfold4: 0.356 Positive Predictive Value CentroidAlifold(20): 0.928 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.759 Vsfold5: 0.365 Sensitivity CentroidAlifold(20): 0.620 Vsfold5: 0.341 Positive Predictive Value CentroidAlifold(20): 0.929 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.907 Alterna: 0.618 Sensitivity CentroidAlifold(20): 0.844 Alterna: 0.626 Positive Predictive Value CentroidAlifold(20): 0.977 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.907 RDfolder: 0.556 Sensitivity CentroidAlifold(20): 0.844 RDfolder: 0.511 Positive Predictive Value CentroidAlifold(20): 0.977 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.819 Carnac(seed): 0.398 Sensitivity CentroidAlifold(20): 0.720 Carnac(seed): 0.173 Positive Predictive Value CentroidAlifold(20): 0.932 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.840 MCFold: 0.500 Sensitivity CentroidAlifold(20): 0.742 MCFold: 0.559 Positive Predictive Value CentroidAlifold(20): 0.953 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.757 RSpredict(seed): 0.410 Sensitivity CentroidAlifold(20): 0.631 RSpredict(seed): 0.277 Positive Predictive Value CentroidAlifold(20): 0.910 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.731 NanoFolder: 0.189 Sensitivity CentroidAlifold(20): 0.584 NanoFolder: 0.218 Positive Predictive Value CentroidAlifold(20): 0.917 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.726 Mastr(seed): 0.104 Sensitivity CentroidAlifold(20): 0.570 Mastr(seed): 0.013 Positive Predictive Value CentroidAlifold(20): 0.926 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidHomfold‑LAST	50 TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.785 CentroidHomfold‑LAST: 0.762 Sensitivity TurboFold(seed): 0.758 CentroidHomfold‑LAST: 0.686 Positive Predictive Value TurboFold(seed): 0.814 CentroidHomfold‑LAST: 0.848 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	1128 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.733 CentroidHomfold‑LAST: 0.698 Sensitivity PETfold_pre2.0(seed): 0.652 CentroidHomfold‑LAST: 0.558 Positive Predictive Value PETfold_pre2.0(seed): 0.827 CentroidHomfold‑LAST: 0.874 Number of pairs reference - predicted secondary structure: 1128 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.749 CentroidHomfold‑LAST: 0.669 Sensitivity ContextFold: 0.712 CentroidHomfold‑LAST: 0.527 Positive Predictive Value ContextFold: 0.789 CentroidHomfold‑LAST: 0.850 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.787 CentroidHomfold‑LAST: 0.749 Sensitivity TurboFold(20): 0.740 CentroidHomfold‑LAST: 0.625 Positive Predictive Value TurboFold(20): 0.837 CentroidHomfold‑LAST: 0.899 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	629 CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 CentroidHomfold‑LAST: 0.699 Sensitivity CentroidAlifold(seed): 0.577 CentroidHomfold‑LAST: 0.561 Positive Predictive Value CentroidAlifold(seed): 0.905 CentroidHomfold‑LAST: 0.872 Number of pairs reference - predicted secondary structure: 629 Wilcoxon single-rank test P-value: 3.56938820447e-08	562 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 CentroidHomfold‑LAST: 0.750 Sensitivity PETfold_pre2.0(20): 0.675 CentroidHomfold‑LAST: 0.626 Positive Predictive Value PETfold_pre2.0(20): 0.870 CentroidHomfold‑LAST: 0.899 Number of pairs reference - predicted secondary structure: 562 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.757 CentroidHomfold‑LAST: 0.749 Sensitivity CentroidAlifold(20): 0.618 CentroidHomfold‑LAST: 0.625 Positive Predictive Value CentroidAlifold(20): 0.928 CentroidHomfold‑LAST: 0.899 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08		- PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.759 CentroidHomfold‑LAST: 0.749 Sensitivity PPfold(20): 0.652 CentroidHomfold‑LAST: 0.624 Positive Predictive Value PPfold(20): 0.885 CentroidHomfold‑LAST: 0.900 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 RNAalifold(20): 0.705 Sensitivity CentroidHomfold‑LAST: 0.625 RNAalifold(20): 0.577 Positive Predictive Value CentroidHomfold‑LAST: 0.899 RNAalifold(20): 0.863 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.701 MXScarna(seed): 0.655 Sensitivity CentroidHomfold‑LAST: 0.563 MXScarna(seed): 0.561 Positive Predictive Value CentroidHomfold‑LAST: 0.873 MXScarna(seed): 0.766 Number of pairs reference - predicted secondary structure: 651 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 MXScarna(20): 0.701 Sensitivity CentroidHomfold‑LAST: 0.625 MXScarna(20): 0.634 Positive Predictive Value CentroidHomfold‑LAST: 0.899 MXScarna(20): 0.776 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 IPknot: 0.635 Sensitivity CentroidHomfold‑LAST: 0.527 IPknot: 0.588 Positive Predictive Value CentroidHomfold‑LAST: 0.850 IPknot: 0.688 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.747 Multilign(20): 0.685 Sensitivity CentroidHomfold‑LAST: 0.622 Multilign(20): 0.617 Positive Predictive Value CentroidHomfold‑LAST: 0.898 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.761 Murlet(20): 0.631 Sensitivity CentroidHomfold‑LAST: 0.648 Murlet(20): 0.496 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Murlet(20): 0.803 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.698 RNAalifold(seed): 0.549 Sensitivity CentroidHomfold‑LAST: 0.559 RNAalifold(seed): 0.352 Positive Predictive Value CentroidHomfold‑LAST: 0.872 RNAalifold(seed): 0.859 Number of pairs reference - predicted secondary structure: 619 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 CentroidFold: 0.602 Sensitivity CentroidHomfold‑LAST: 0.527 CentroidFold: 0.555 Positive Predictive Value CentroidHomfold‑LAST: 0.850 CentroidFold: 0.653 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.794 RNASampler(20): 0.676 Sensitivity CentroidHomfold‑LAST: 0.706 RNASampler(20): 0.522 Positive Predictive Value CentroidHomfold‑LAST: 0.894 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 Contrafold: 0.588 Sensitivity CentroidHomfold‑LAST: 0.527 Contrafold: 0.578 Positive Predictive Value CentroidHomfold‑LAST: 0.850 Contrafold: 0.600 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 Sfold: 0.562 Sensitivity CentroidHomfold‑LAST: 0.527 Sfold: 0.516 Positive Predictive Value CentroidHomfold‑LAST: 0.850 Sfold: 0.614 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.684 Multilign(seed): 0.681 Sensitivity CentroidHomfold‑LAST: 0.581 Multilign(seed): 0.649 Positive Predictive Value CentroidHomfold‑LAST: 0.806 Multilign(seed): 0.717 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.00027446829016	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 MaxExpect: 0.562 Sensitivity CentroidHomfold‑LAST: 0.527 MaxExpect: 0.551 Positive Predictive Value CentroidHomfold‑LAST: 0.850 MaxExpect: 0.576 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 ProbKnot: 0.561 Sensitivity CentroidHomfold‑LAST: 0.527 ProbKnot: 0.556 Positive Predictive Value CentroidHomfold‑LAST: 0.850 ProbKnot: 0.567 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 Fold: 0.543 Sensitivity CentroidHomfold‑LAST: 0.527 Fold: 0.545 Positive Predictive Value CentroidHomfold‑LAST: 0.850 Fold: 0.543 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.742 RNASampler(seed): 0.629 Sensitivity CentroidHomfold‑LAST: 0.664 RNASampler(seed): 0.468 Positive Predictive Value CentroidHomfold‑LAST: 0.831 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 UNAFold: 0.533 Sensitivity CentroidHomfold‑LAST: 0.527 UNAFold: 0.528 Positive Predictive Value CentroidHomfold‑LAST: 0.850 UNAFold: 0.539 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 RNAsubopt: 0.525 Sensitivity CentroidHomfold‑LAST: 0.527 RNAsubopt: 0.530 Positive Predictive Value CentroidHomfold‑LAST: 0.850 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 RSpredict(20): 0.524 Sensitivity CentroidHomfold‑LAST: 0.625 RSpredict(20): 0.385 Positive Predictive Value CentroidHomfold‑LAST: 0.899 RSpredict(20): 0.714 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 CMfinder(20): 0.549 Sensitivity CentroidHomfold‑LAST: 0.624 CMfinder(20): 0.380 Positive Predictive Value CentroidHomfold‑LAST: 0.899 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 PknotsRG: 0.530 Sensitivity CentroidHomfold‑LAST: 0.527 PknotsRG: 0.530 Positive Predictive Value CentroidHomfold‑LAST: 0.850 PknotsRG: 0.531 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 Carnac(20): 0.469 Sensitivity CentroidHomfold‑LAST: 0.625 Carnac(20): 0.248 Positive Predictive Value CentroidHomfold‑LAST: 0.899 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 RNAfold: 0.531 Sensitivity CentroidHomfold‑LAST: 0.527 RNAfold: 0.531 Positive Predictive Value CentroidHomfold‑LAST: 0.850 RNAfold: 0.533 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.725 CMfinder(seed): 0.486 Sensitivity CentroidHomfold‑LAST: 0.598 CMfinder(seed): 0.312 Positive Predictive Value CentroidHomfold‑LAST: 0.880 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.664 Afold: 0.537 Sensitivity CentroidHomfold‑LAST: 0.525 Afold: 0.531 Positive Predictive Value CentroidHomfold‑LAST: 0.840 Afold: 0.545 Number of pairs reference - predicted secondary structure: 1002 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.735 HotKnots: 0.613 Sensitivity CentroidHomfold‑LAST: 0.665 HotKnots: 0.607 Positive Predictive Value CentroidHomfold‑LAST: 0.815 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 CRWrnafold: 0.480 Sensitivity CentroidHomfold‑LAST: 0.527 CRWrnafold: 0.481 Positive Predictive Value CentroidHomfold‑LAST: 0.850 CRWrnafold: 0.482 Number of pairs reference - predicted secondary structure: 1640 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.745 Pknots: 0.606 Sensitivity CentroidHomfold‑LAST: 0.685 Pknots: 0.595 Positive Predictive Value CentroidHomfold‑LAST: 0.815 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 McQFold: 0.479 Sensitivity CentroidHomfold‑LAST: 0.527 McQFold: 0.466 Positive Predictive Value CentroidHomfold‑LAST: 0.850 McQFold: 0.494 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.673 RNAshapes: 0.477 Sensitivity CentroidHomfold‑LAST: 0.534 RNAshapes: 0.472 Positive Predictive Value CentroidHomfold‑LAST: 0.850 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 PPfold(seed): 0.635 Sensitivity CentroidHomfold‑LAST: 0.676 PPfold(seed): 0.511 Positive Predictive Value CentroidHomfold‑LAST: 0.830 PPfold(seed): 0.790 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 Mastr(20): 0.350 Sensitivity CentroidHomfold‑LAST: 0.625 Mastr(20): 0.156 Positive Predictive Value CentroidHomfold‑LAST: 0.899 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.727 Murlet(seed): 0.519 Sensitivity CentroidHomfold‑LAST: 0.631 Murlet(seed): 0.322 Positive Predictive Value CentroidHomfold‑LAST: 0.840 Murlet(seed): 0.839 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.679 RNASLOpt: 0.471 Sensitivity CentroidHomfold‑LAST: 0.544 RNASLOpt: 0.444 Positive Predictive Value CentroidHomfold‑LAST: 0.847 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1542 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.765 Cylofold: 0.575 Sensitivity CentroidHomfold‑LAST: 0.706 Cylofold: 0.551 Positive Predictive Value CentroidHomfold‑LAST: 0.832 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 RNAwolf: 0.384 Sensitivity CentroidHomfold‑LAST: 0.527 RNAwolf: 0.397 Positive Predictive Value CentroidHomfold‑LAST: 0.850 RNAwolf: 0.373 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.673 Vsfold4: 0.346 Sensitivity CentroidHomfold‑LAST: 0.534 Vsfold4: 0.318 Positive Predictive Value CentroidHomfold‑LAST: 0.850 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.674 Vsfold5: 0.339 Sensitivity CentroidHomfold‑LAST: 0.534 Vsfold5: 0.322 Positive Predictive Value CentroidHomfold‑LAST: 0.850 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.748 Alterna: 0.552 Sensitivity CentroidHomfold‑LAST: 0.687 Alterna: 0.547 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.748 RDfolder: 0.520 Sensitivity CentroidHomfold‑LAST: 0.687 RDfolder: 0.464 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.688 Carnac(seed): 0.224 Sensitivity CentroidHomfold‑LAST: 0.577 Carnac(seed): 0.057 Positive Predictive Value CentroidHomfold‑LAST: 0.821 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 MCFold: 0.473 Sensitivity CentroidHomfold‑LAST: 0.671 MCFold: 0.524 Positive Predictive Value CentroidHomfold‑LAST: 0.812 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.699 RSpredict(seed): 0.236 Sensitivity CentroidHomfold‑LAST: 0.561 RSpredict(seed): 0.105 Positive Predictive Value CentroidHomfold‑LAST: 0.872 RSpredict(seed): 0.530 Number of pairs reference - predicted secondary structure: 632 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.679 NanoFolder: 0.198 Sensitivity CentroidHomfold‑LAST: 0.527 NanoFolder: 0.233 Positive Predictive Value CentroidHomfold‑LAST: 0.876 NanoFolder: 0.171 Number of pairs reference - predicted secondary structure: 248 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 Mastr(seed): 0.117 Sensitivity CentroidHomfold‑LAST: 0.569 Mastr(seed): 0.017 Positive Predictive Value CentroidHomfold‑LAST: 0.870 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 628 Wilcoxon single-rank test P-value: 3.56938820447e-08
PPfold(20)	19 TurboFold(seed) vs PPfold(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 PPfold(20): 0.582 Sensitivity TurboFold(seed): 0.851 PPfold(20): 0.365 Positive Predictive Value TurboFold(seed): 0.867 PPfold(20): 0.933 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.02510705504e-08	542 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.799 PPfold(20): 0.766 Sensitivity PETfold_pre2.0(seed): 0.732 PPfold(20): 0.669 Positive Predictive Value PETfold_pre2.0(seed): 0.873 PPfold(20): 0.879 Number of pairs reference - predicted secondary structure: 542 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 ContextFold vs PPfold(20) Matthews Correlation Coefficient ContextFold: 0.855 PPfold(20): 0.758 Sensitivity ContextFold: 0.814 PPfold(20): 0.654 Positive Predictive Value ContextFold: 0.898 PPfold(20): 0.879 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	552 TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.787 PPfold(20): 0.759 Sensitivity TurboFold(20): 0.740 PPfold(20): 0.652 Positive Predictive Value TurboFold(20): 0.838 PPfold(20): 0.885 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	335 CentroidAlifold(seed) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.753 PPfold(20): 0.739 Sensitivity CentroidAlifold(seed): 0.603 PPfold(20): 0.627 Positive Predictive Value CentroidAlifold(seed): 0.942 PPfold(20): 0.873 Number of pairs reference - predicted secondary structure: 335 Wilcoxon single-rank test P-value: 3.56938820447e-08	555 PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 PPfold(20): 0.760 Sensitivity PETfold_pre2.0(20): 0.681 PPfold(20): 0.657 Positive Predictive Value PETfold_pre2.0(20): 0.862 PPfold(20): 0.879 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(20): 0.758 CentroidAlifold(20): 0.758 Sensitivity PPfold(20): 0.654 CentroidAlifold(20): 0.622 Positive Predictive Value PPfold(20): 0.879 CentroidAlifold(20): 0.924 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 0.00586086047676	552 PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.759 CentroidHomfold‑LAST: 0.749 Sensitivity PPfold(20): 0.652 CentroidHomfold‑LAST: 0.624 Positive Predictive Value PPfold(20): 0.885 CentroidHomfold‑LAST: 0.900 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.758 RNAalifold(20): 0.704 Sensitivity PPfold(20): 0.654 RNAalifold(20): 0.583 Positive Predictive Value PPfold(20): 0.879 RNAalifold(20): 0.852 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.742 MXScarna(seed): 0.705 Sensitivity PPfold(20): 0.630 MXScarna(seed): 0.611 Positive Predictive Value PPfold(20): 0.875 MXScarna(seed): 0.813 Number of pairs reference - predicted secondary structure: 349 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.758 MXScarna(20): 0.697 Sensitivity PPfold(20): 0.654 MXScarna(20): 0.632 Positive Predictive Value PPfold(20): 0.879 MXScarna(20): 0.770 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.758 IPknot: 0.677 Sensitivity PPfold(20): 0.654 IPknot: 0.616 Positive Predictive Value PPfold(20): 0.879 IPknot: 0.746 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.763 Multilign(20): 0.687 Sensitivity PPfold(20): 0.656 Multilign(20): 0.620 Positive Predictive Value PPfold(20): 0.888 Multilign(20): 0.763 Number of pairs reference - predicted secondary structure: 522 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.767 Murlet(20): 0.634 Sensitivity PPfold(20): 0.664 Murlet(20): 0.500 Positive Predictive Value PPfold(20): 0.888 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 487 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.733 RNAalifold(seed): 0.533 Sensitivity PPfold(20): 0.621 RNAalifold(seed): 0.339 Positive Predictive Value PPfold(20): 0.865 RNAalifold(seed): 0.839 Number of pairs reference - predicted secondary structure: 333 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.758 CentroidFold: 0.637 Sensitivity PPfold(20): 0.654 CentroidFold: 0.579 Positive Predictive Value PPfold(20): 0.879 CentroidFold: 0.702 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.769 RNASampler(20): 0.677 Sensitivity PPfold(20): 0.648 RNASampler(20): 0.524 Positive Predictive Value PPfold(20): 0.912 RNASampler(20): 0.876 Number of pairs reference - predicted secondary structure: 388 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.758 Contrafold: 0.624 Sensitivity PPfold(20): 0.654 Contrafold: 0.605 Positive Predictive Value PPfold(20): 0.879 Contrafold: 0.644 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.758 Sfold: 0.603 Sensitivity PPfold(20): 0.654 Sfold: 0.542 Positive Predictive Value PPfold(20): 0.879 Sfold: 0.671 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.531 Multilign(seed): 0.334 Sensitivity PPfold(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value PPfold(20): 0.875 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.758 MaxExpect: 0.603 Sensitivity PPfold(20): 0.654 MaxExpect: 0.583 Positive Predictive Value PPfold(20): 0.879 MaxExpect: 0.625 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.758 ProbKnot: 0.601 Sensitivity PPfold(20): 0.654 ProbKnot: 0.585 Positive Predictive Value PPfold(20): 0.879 ProbKnot: 0.618 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.758 Fold: 0.580 Sensitivity PPfold(20): 0.654 Fold: 0.574 Positive Predictive Value PPfold(20): 0.879 Fold: 0.587 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(20): 0.690 RNASampler(seed): 0.571 Sensitivity PPfold(20): 0.547 RNASampler(seed): 0.343 Positive Predictive Value PPfold(20): 0.876 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.758 UNAFold: 0.575 Sensitivity PPfold(20): 0.654 UNAFold: 0.563 Positive Predictive Value PPfold(20): 0.879 UNAFold: 0.588 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.759 RNAsubopt: 0.570 Sensitivity PPfold(20): 0.652 RNAsubopt: 0.569 Positive Predictive Value PPfold(20): 0.885 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.758 RSpredict(20): 0.526 Sensitivity PPfold(20): 0.654 RSpredict(20): 0.396 Positive Predictive Value PPfold(20): 0.879 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.760 CMfinder(20): 0.551 Sensitivity PPfold(20): 0.654 CMfinder(20): 0.382 Positive Predictive Value PPfold(20): 0.885 CMfinder(20): 0.795 Number of pairs reference - predicted secondary structure: 549 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.763 PknotsRG: 0.559 Sensitivity PPfold(20): 0.658 PknotsRG: 0.551 Positive Predictive Value PPfold(20): 0.885 PknotsRG: 0.568 Number of pairs reference - predicted secondary structure: 556 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.758 Carnac(20): 0.482 Sensitivity PPfold(20): 0.654 Carnac(20): 0.260 Positive Predictive Value PPfold(20): 0.879 Carnac(20): 0.896 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.758 RNAfold: 0.566 Sensitivity PPfold(20): 0.654 RNAfold: 0.559 Positive Predictive Value PPfold(20): 0.879 RNAfold: 0.575 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs PPfold(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 PPfold(20): 0.656 Sensitivity CMfinder(seed): 0.607 PPfold(20): 0.507 Positive Predictive Value CMfinder(seed): 0.898 PPfold(20): 0.856 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.740 Afold: 0.556 Sensitivity PPfold(20): 0.631 Afold: 0.544 Positive Predictive Value PPfold(20): 0.869 Afold: 0.570 Number of pairs reference - predicted secondary structure: 342 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.839 HotKnots: 0.696 Sensitivity PPfold(20): 0.721 HotKnots: 0.692 Positive Predictive Value PPfold(20): 0.977 HotKnots: 0.704 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.762 CRWrnafold: 0.545 Sensitivity PPfold(20): 0.656 CRWrnafold: 0.536 Positive Predictive Value PPfold(20): 0.885 CRWrnafold: 0.556 Number of pairs reference - predicted secondary structure: 554 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.882 Pknots: 0.664 Sensitivity PPfold(20): 0.796 Pknots: 0.671 Positive Predictive Value PPfold(20): 0.979 Pknots: 0.662 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.759 McQFold: 0.484 Sensitivity PPfold(20): 0.652 McQFold: 0.464 Positive Predictive Value PPfold(20): 0.885 McQFold: 0.508 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.762 RNAshapes: 0.526 Sensitivity PPfold(20): 0.655 RNAshapes: 0.513 Positive Predictive Value PPfold(20): 0.889 RNAshapes: 0.540 Number of pairs reference - predicted secondary structure: 543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.640 PPfold(seed): 0.453 Sensitivity PPfold(20): 0.434 PPfold(seed): 0.224 Positive Predictive Value PPfold(20): 0.947 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.754 Mastr(20): 0.349 Sensitivity PPfold(20): 0.648 Mastr(20): 0.154 Positive Predictive Value PPfold(20): 0.879 Mastr(20): 0.792 Number of pairs reference - predicted secondary structure: 554 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.695 Murlet(seed): 0.631 Sensitivity PPfold(20): 0.546 Murlet(seed): 0.418 Positive Predictive Value PPfold(20): 0.889 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.763 RNASLOpt: 0.501 Sensitivity PPfold(20): 0.656 RNASLOpt: 0.464 Positive Predictive Value PPfold(20): 0.888 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 536 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.837 Cylofold: 0.560 Sensitivity PPfold(20): 0.719 Cylofold: 0.546 Positive Predictive Value PPfold(20): 0.976 Cylofold: 0.579 Number of pairs reference - predicted secondary structure: 298 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.759 RNAwolf: 0.415 Sensitivity PPfold(20): 0.652 RNAwolf: 0.424 Positive Predictive Value PPfold(20): 0.885 RNAwolf: 0.409 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.761 Vsfold4: 0.392 Sensitivity PPfold(20): 0.654 Vsfold4: 0.357 Positive Predictive Value PPfold(20): 0.887 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 548 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.762 Vsfold5: 0.366 Sensitivity PPfold(20): 0.655 Vsfold5: 0.342 Positive Predictive Value PPfold(20): 0.887 Vsfold5: 0.395 Number of pairs reference - predicted secondary structure: 545 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.884 Alterna: 0.618 Sensitivity PPfold(20): 0.800 Alterna: 0.626 Positive Predictive Value PPfold(20): 0.979 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.884 RDfolder: 0.562 Sensitivity PPfold(20): 0.800 RDfolder: 0.517 Positive Predictive Value PPfold(20): 0.979 RDfolder: 0.618 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.732 Carnac(seed): 0.317 Sensitivity PPfold(20): 0.596 Carnac(seed): 0.111 Positive Predictive Value PPfold(20): 0.900 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.830 MCFold: 0.500 Sensitivity PPfold(20): 0.707 MCFold: 0.560 Positive Predictive Value PPfold(20): 0.976 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.740 RSpredict(seed): 0.288 Sensitivity PPfold(20): 0.627 RSpredict(seed): 0.140 Positive Predictive Value PPfold(20): 0.874 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 337 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.735 NanoFolder: 0.192 Sensitivity PPfold(20): 0.619 NanoFolder: 0.221 Positive Predictive Value PPfold(20): 0.873 NanoFolder: 0.170 Number of pairs reference - predicted secondary structure: 113 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.736 Mastr(seed): 0.108 Sensitivity PPfold(20): 0.619 Mastr(seed): 0.014 Positive Predictive Value PPfold(20): 0.876 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 331 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(20)	19 TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 RNAalifold(20): 0.622 Sensitivity TurboFold(seed): 0.851 RNAalifold(20): 0.435 Positive Predictive Value TurboFold(seed): 0.867 RNAalifold(20): 0.893 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	626 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 RNAalifold(20): 0.689 Sensitivity PETfold_pre2.0(seed): 0.729 RNAalifold(20): 0.604 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RNAalifold(20): 0.786 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.791 RNAalifold(20): 0.687 Sensitivity ContextFold: 0.752 RNAalifold(20): 0.600 Positive Predictive Value ContextFold: 0.832 RNAalifold(20): 0.787 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.787 RNAalifold(20): 0.705 Sensitivity TurboFold(20): 0.740 RNAalifold(20): 0.577 Positive Predictive Value TurboFold(20): 0.837 RNAalifold(20): 0.863 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 RNAalifold(20): 0.716 Sensitivity CentroidAlifold(seed): 0.652 RNAalifold(20): 0.621 Positive Predictive Value CentroidAlifold(seed): 0.918 RNAalifold(20): 0.825 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 RNAalifold(20): 0.687 Sensitivity PETfold_pre2.0(20): 0.686 RNAalifold(20): 0.601 Positive Predictive Value PETfold_pre2.0(20): 0.807 RNAalifold(20): 0.787 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.740 RNAalifold(20): 0.687 Sensitivity CentroidAlifold(20): 0.616 RNAalifold(20): 0.600 Positive Predictive Value CentroidAlifold(20): 0.891 RNAalifold(20): 0.787 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 RNAalifold(20): 0.705 Sensitivity CentroidHomfold‑LAST: 0.625 RNAalifold(20): 0.577 Positive Predictive Value CentroidHomfold‑LAST: 0.899 RNAalifold(20): 0.863 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.758 RNAalifold(20): 0.704 Sensitivity PPfold(20): 0.654 RNAalifold(20): 0.583 Positive Predictive Value PPfold(20): 0.879 RNAalifold(20): 0.852 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.717 MXScarna(seed): 0.682 Sensitivity RNAalifold(20): 0.622 MXScarna(seed): 0.601 Positive Predictive Value RNAalifold(20): 0.826 MXScarna(seed): 0.774 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.687 MXScarna(20): 0.647 Sensitivity RNAalifold(20): 0.600 MXScarna(20): 0.589 Positive Predictive Value RNAalifold(20): 0.787 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.687 IPknot: 0.609 Sensitivity RNAalifold(20): 0.600 IPknot: 0.546 Positive Predictive Value RNAalifold(20): 0.787 IPknot: 0.679 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.707 Multilign(20): 0.685 Sensitivity RNAalifold(20): 0.578 Multilign(20): 0.617 Positive Predictive Value RNAalifold(20): 0.866 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.714 Murlet(20): 0.629 Sensitivity RNAalifold(20): 0.603 Murlet(20): 0.503 Positive Predictive Value RNAalifold(20): 0.846 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.704 RNAalifold(seed): 0.648 Sensitivity RNAalifold(20): 0.611 RNAalifold(seed): 0.508 Positive Predictive Value RNAalifold(20): 0.812 RNAalifold(seed): 0.826 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.689 CentroidFold: 0.569 Sensitivity RNAalifold(20): 0.602 CentroidFold: 0.508 Positive Predictive Value RNAalifold(20): 0.789 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.744 RNASampler(20): 0.676 Sensitivity RNAalifold(20): 0.623 RNASampler(20): 0.522 Positive Predictive Value RNAalifold(20): 0.889 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.687 Contrafold: 0.554 Sensitivity RNAalifold(20): 0.600 Contrafold: 0.536 Positive Predictive Value RNAalifold(20): 0.787 Contrafold: 0.572 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.687 Sfold: 0.530 Sensitivity RNAalifold(20): 0.600 Sfold: 0.475 Positive Predictive Value RNAalifold(20): 0.787 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): 0.568 Multilign(seed): 0.334 Sensitivity RNAalifold(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value RNAalifold(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.687 MaxExpect: 0.512 Sensitivity RNAalifold(20): 0.600 MaxExpect: 0.499 Positive Predictive Value RNAalifold(20): 0.787 MaxExpect: 0.527 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.687 ProbKnot: 0.507 Sensitivity RNAalifold(20): 0.600 ProbKnot: 0.498 Positive Predictive Value RNAalifold(20): 0.787 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.687 Fold: 0.485 Sensitivity RNAalifold(20): 0.600 Fold: 0.486 Positive Predictive Value RNAalifold(20): 0.787 Fold: 0.485 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(20): 0.659 RNASampler(seed): 0.571 Sensitivity RNAalifold(20): 0.511 RNASampler(seed): 0.343 Positive Predictive Value RNAalifold(20): 0.857 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.687 UNAFold: 0.497 Sensitivity RNAalifold(20): 0.600 UNAFold: 0.491 Positive Predictive Value RNAalifold(20): 0.787 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.705 RNAsubopt: 0.570 Sensitivity RNAalifold(20): 0.577 RNAsubopt: 0.570 Positive Predictive Value RNAalifold(20): 0.863 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.687 RSpredict(20): 0.487 Sensitivity RNAalifold(20): 0.600 RSpredict(20): 0.402 Positive Predictive Value RNAalifold(20): 0.787 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.706 CMfinder(20): 0.549 Sensitivity RNAalifold(20): 0.578 CMfinder(20): 0.380 Positive Predictive Value RNAalifold(20): 0.863 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.752 PknotsRG: 0.521 Sensitivity RNAalifold(20): 0.655 PknotsRG: 0.514 Positive Predictive Value RNAalifold(20): 0.864 PknotsRG: 0.529 Number of pairs reference - predicted secondary structure: 611 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.687 Carnac(20): 0.518 Sensitivity RNAalifold(20): 0.600 Carnac(20): 0.301 Positive Predictive Value RNAalifold(20): 0.787 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.687 RNAfold: 0.482 Sensitivity RNAalifold(20): 0.600 RNAfold: 0.480 Positive Predictive Value RNAalifold(20): 0.787 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs RNAalifold(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RNAalifold(20): 0.620 Sensitivity CMfinder(seed): 0.607 RNAalifold(20): 0.466 Positive Predictive Value CMfinder(seed): 0.898 RNAalifold(20): 0.832 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.676 Afold: 0.474 Sensitivity RNAalifold(20): 0.589 Afold: 0.470 Positive Predictive Value RNAalifold(20): 0.775 Afold: 0.479 Number of pairs reference - predicted secondary structure: 421 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.816 HotKnots: 0.698 Sensitivity RNAalifold(20): 0.690 HotKnots: 0.695 Positive Predictive Value RNAalifold(20): 0.966 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.738 CRWrnafold: 0.541 Sensitivity RNAalifold(20): 0.631 CRWrnafold: 0.532 Positive Predictive Value RNAalifold(20): 0.865 CRWrnafold: 0.551 Number of pairs reference - predicted secondary structure: 590 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.881 Pknots: 0.655 Sensitivity RNAalifold(20): 0.794 Pknots: 0.662 Positive Predictive Value RNAalifold(20): 0.980 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.705 McQFold: 0.484 Sensitivity RNAalifold(20): 0.577 McQFold: 0.464 Positive Predictive Value RNAalifold(20): 0.863 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.708 RNAshapes: 0.526 Sensitivity RNAalifold(20): 0.580 RNAshapes: 0.514 Positive Predictive Value RNAalifold(20): 0.867 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.704 PPfold(seed): 0.453 Sensitivity RNAalifold(20): 0.524 PPfold(seed): 0.224 Positive Predictive Value RNAalifold(20): 0.948 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.85839946686e-08	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.625 Mastr(20): 0.296 Sensitivity RNAalifold(20): 0.523 Mastr(20): 0.111 Positive Predictive Value RNAalifold(20): 0.747 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.672 Murlet(seed): 0.631 Sensitivity RNAalifold(20): 0.518 Murlet(seed): 0.418 Positive Predictive Value RNAalifold(20): 0.876 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.710 RNASLOpt: 0.500 Sensitivity RNAalifold(20): 0.582 RNASLOpt: 0.464 Positive Predictive Value RNAalifold(20): 0.866 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.816 Cylofold: 0.557 Sensitivity RNAalifold(20): 0.690 Cylofold: 0.543 Positive Predictive Value RNAalifold(20): 0.968 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.705 RNAwolf: 0.414 Sensitivity RNAalifold(20): 0.577 RNAwolf: 0.423 Positive Predictive Value RNAalifold(20): 0.863 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.707 Vsfold4: 0.390 Sensitivity RNAalifold(20): 0.579 Vsfold4: 0.356 Positive Predictive Value RNAalifold(20): 0.865 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.708 Vsfold5: 0.365 Sensitivity RNAalifold(20): 0.580 Vsfold5: 0.341 Positive Predictive Value RNAalifold(20): 0.866 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.883 Alterna: 0.618 Sensitivity RNAalifold(20): 0.795 Alterna: 0.626 Positive Predictive Value RNAalifold(20): 0.982 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.883 RDfolder: 0.556 Sensitivity RNAalifold(20): 0.795 RDfolder: 0.511 Positive Predictive Value RNAalifold(20): 0.982 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.730 Carnac(seed): 0.398 Sensitivity RNAalifold(20): 0.600 Carnac(seed): 0.173 Positive Predictive Value RNAalifold(20): 0.889 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.817 MCFold: 0.500 Sensitivity RNAalifold(20): 0.689 MCFold: 0.559 Positive Predictive Value RNAalifold(20): 0.970 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.710 RSpredict(seed): 0.410 Sensitivity RNAalifold(20): 0.613 RSpredict(seed): 0.277 Positive Predictive Value RNAalifold(20): 0.823 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.684 NanoFolder: 0.189 Sensitivity RNAalifold(20): 0.554 NanoFolder: 0.218 Positive Predictive Value RNAalifold(20): 0.846 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.664 Mastr(seed): 0.104 Sensitivity RNAalifold(20): 0.527 Mastr(seed): 0.013 Positive Predictive Value RNAalifold(20): 0.836 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(seed)	51 TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.791 MXScarna(seed): 0.734 Sensitivity TurboFold(seed): 0.762 MXScarna(seed): 0.698 Positive Predictive Value TurboFold(seed): 0.822 MXScarna(seed): 0.773 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	710 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.765 MXScarna(seed): 0.652 Sensitivity PETfold_pre2.0(seed): 0.702 MXScarna(seed): 0.566 Positive Predictive Value PETfold_pre2.0(seed): 0.835 MXScarna(seed): 0.752 Number of pairs reference - predicted secondary structure: 710 Wilcoxon single-rank test P-value: 3.56938820447e-08	728 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.812 MXScarna(seed): 0.654 Sensitivity ContextFold: 0.774 MXScarna(seed): 0.568 Positive Predictive Value ContextFold: 0.853 MXScarna(seed): 0.753 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	358 TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.781 MXScarna(seed): 0.701 Sensitivity TurboFold(20): 0.733 MXScarna(seed): 0.607 Positive Predictive Value TurboFold(20): 0.833 MXScarna(seed): 0.810 Number of pairs reference - predicted secondary structure: 358 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 MXScarna(seed): 0.653 Sensitivity CentroidAlifold(seed): 0.623 MXScarna(seed): 0.567 Positive Predictive Value CentroidAlifold(seed): 0.901 MXScarna(seed): 0.752 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	413 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 MXScarna(seed): 0.682 Sensitivity PETfold_pre2.0(20): 0.703 MXScarna(seed): 0.601 Positive Predictive Value PETfold_pre2.0(20): 0.835 MXScarna(seed): 0.774 Number of pairs reference - predicted secondary structure: 413 Wilcoxon single-rank test P-value: 3.56938820447e-08	416 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.762 MXScarna(seed): 0.682 Sensitivity CentroidAlifold(20): 0.639 MXScarna(seed): 0.601 Positive Predictive Value CentroidAlifold(20): 0.909 MXScarna(seed): 0.774 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	651 CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.701 MXScarna(seed): 0.655 Sensitivity CentroidHomfold‑LAST: 0.563 MXScarna(seed): 0.561 Positive Predictive Value CentroidHomfold‑LAST: 0.873 MXScarna(seed): 0.766 Number of pairs reference - predicted secondary structure: 651 Wilcoxon single-rank test P-value: 3.56938820447e-08	349 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.742 MXScarna(seed): 0.705 Sensitivity PPfold(20): 0.630 MXScarna(seed): 0.611 Positive Predictive Value PPfold(20): 0.875 MXScarna(seed): 0.813 Number of pairs reference - predicted secondary structure: 349 Wilcoxon single-rank test P-value: 3.56938820447e-08	416 RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.717 MXScarna(seed): 0.682 Sensitivity RNAalifold(20): 0.622 MXScarna(seed): 0.601 Positive Predictive Value RNAalifold(20): 0.826 MXScarna(seed): 0.774 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.682 MXScarna(20): 0.670 Sensitivity MXScarna(seed): 0.601 MXScarna(20): 0.602 Positive Predictive Value MXScarna(seed): 0.774 MXScarna(20): 0.746 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.654 IPknot: 0.633 Sensitivity MXScarna(seed): 0.568 IPknot: 0.571 Positive Predictive Value MXScarna(seed): 0.753 IPknot: 0.703 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.697 Multilign(20): 0.653 Sensitivity MXScarna(seed): 0.600 Multilign(20): 0.577 Positive Predictive Value MXScarna(seed): 0.810 Multilign(20): 0.741 Number of pairs reference - predicted secondary structure: 330 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.702 Murlet(20): 0.592 Sensitivity MXScarna(seed): 0.620 Murlet(20): 0.454 Positive Predictive Value MXScarna(seed): 0.794 Murlet(20): 0.773 Number of pairs reference - predicted secondary structure: 297 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.652 RNAalifold(seed): 0.640 Sensitivity MXScarna(seed): 0.566 RNAalifold(seed): 0.485 Positive Predictive Value MXScarna(seed): 0.752 RNAalifold(seed): 0.844 Number of pairs reference - predicted secondary structure: 696 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.656 CentroidFold: 0.599 Sensitivity MXScarna(seed): 0.570 CentroidFold: 0.539 Positive Predictive Value MXScarna(seed): 0.756 CentroidFold: 0.667 Number of pairs reference - predicted secondary structure: 727 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.788 RNASampler(20): 0.605 Sensitivity MXScarna(seed): 0.740 RNASampler(20): 0.405 Positive Predictive Value MXScarna(seed): 0.840 RNASampler(20): 0.904 Number of pairs reference - predicted secondary structure: 190 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.654 Contrafold: 0.585 Sensitivity MXScarna(seed): 0.568 Contrafold: 0.566 Positive Predictive Value MXScarna(seed): 0.753 Contrafold: 0.605 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.654 Sfold: 0.571 Sensitivity MXScarna(seed): 0.568 Sfold: 0.515 Positive Predictive Value MXScarna(seed): 0.753 Sfold: 0.633 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.698 MXScarna(seed): 0.686 Sensitivity Multilign(seed): 0.660 MXScarna(seed): 0.662 Positive Predictive Value Multilign(seed): 0.741 MXScarna(seed): 0.712 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 1.27663599501e-06	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.654 MaxExpect: 0.545 Sensitivity MXScarna(seed): 0.568 MaxExpect: 0.530 Positive Predictive Value MXScarna(seed): 0.753 MaxExpect: 0.561 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.654 ProbKnot: 0.541 Sensitivity MXScarna(seed): 0.568 ProbKnot: 0.530 Positive Predictive Value MXScarna(seed): 0.753 ProbKnot: 0.553 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.654 Fold: 0.520 Sensitivity MXScarna(seed): 0.568 Fold: 0.518 Positive Predictive Value MXScarna(seed): 0.753 Fold: 0.522 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.738 RNASampler(seed): 0.629 Sensitivity MXScarna(seed): 0.703 RNASampler(seed): 0.468 Positive Predictive Value MXScarna(seed): 0.777 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.654 UNAFold: 0.536 Sensitivity MXScarna(seed): 0.568 UNAFold: 0.528 Positive Predictive Value MXScarna(seed): 0.753 UNAFold: 0.546 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.655 RNAsubopt: 0.570 Sensitivity MXScarna(seed): 0.561 RNAsubopt: 0.571 Positive Predictive Value MXScarna(seed): 0.766 RNAsubopt: 0.571 Number of pairs reference - predicted secondary structure: 651 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.682 RSpredict(20): 0.533 Sensitivity MXScarna(seed): 0.601 RSpredict(20): 0.425 Positive Predictive Value MXScarna(seed): 0.774 RSpredict(20): 0.668 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.701 CMfinder(20): 0.524 Sensitivity MXScarna(seed): 0.607 CMfinder(20): 0.354 Positive Predictive Value MXScarna(seed): 0.810 CMfinder(20): 0.777 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.668 PknotsRG: 0.529 Sensitivity MXScarna(seed): 0.579 PknotsRG: 0.524 Positive Predictive Value MXScarna(seed): 0.772 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 716 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.682 Carnac(20): 0.508 Sensitivity MXScarna(seed): 0.601 Carnac(20): 0.285 Positive Predictive Value MXScarna(seed): 0.774 Carnac(20): 0.903 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.654 RNAfold: 0.521 Sensitivity MXScarna(seed): 0.568 RNAfold: 0.516 Positive Predictive Value MXScarna(seed): 0.753 RNAfold: 0.526 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CMfinder(seed) Matthews Correlation Coefficient MXScarna(seed): 0.697 CMfinder(seed): 0.486 Sensitivity MXScarna(seed): 0.619 CMfinder(seed): 0.312 Positive Predictive Value MXScarna(seed): 0.785 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.651 Afold: 0.515 Sensitivity MXScarna(seed): 0.564 Afold: 0.508 Positive Predictive Value MXScarna(seed): 0.752 Afold: 0.522 Number of pairs reference - predicted secondary structure: 584 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.751 HotKnots: 0.677 Sensitivity MXScarna(seed): 0.714 HotKnots: 0.678 Positive Predictive Value MXScarna(seed): 0.792 HotKnots: 0.680 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.662 CRWrnafold: 0.509 Sensitivity MXScarna(seed): 0.571 CRWrnafold: 0.504 Positive Predictive Value MXScarna(seed): 0.769 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.748 Pknots: 0.532 Sensitivity MXScarna(seed): 0.715 Pknots: 0.527 Positive Predictive Value MXScarna(seed): 0.787 Pknots: 0.545 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.651 McQFold: 0.478 Sensitivity MXScarna(seed): 0.556 McQFold: 0.460 Positive Predictive Value MXScarna(seed): 0.764 McQFold: 0.498 Number of pairs reference - predicted secondary structure: 664 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.662 RNAshapes: 0.527 Sensitivity MXScarna(seed): 0.570 RNAshapes: 0.516 Positive Predictive Value MXScarna(seed): 0.771 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.720 PPfold(seed): 0.626 Sensitivity MXScarna(seed): 0.692 PPfold(seed): 0.495 Positive Predictive Value MXScarna(seed): 0.751 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.665 Mastr(20): 0.239 Sensitivity MXScarna(seed): 0.582 Mastr(20): 0.069 Positive Predictive Value MXScarna(seed): 0.760 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 367 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.731 Murlet(seed): 0.540 Sensitivity MXScarna(seed): 0.700 Murlet(seed): 0.360 Positive Predictive Value MXScarna(seed): 0.763 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.675 RNASLOpt: 0.480 Sensitivity MXScarna(seed): 0.587 RNASLOpt: 0.447 Positive Predictive Value MXScarna(seed): 0.778 RNASLOpt: 0.517 Number of pairs reference - predicted secondary structure: 603 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.760 Cylofold: 0.520 Sensitivity MXScarna(seed): 0.725 Cylofold: 0.495 Positive Predictive Value MXScarna(seed): 0.801 Cylofold: 0.552 Number of pairs reference - predicted secondary structure: 214 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.651 RNAwolf: 0.395 Sensitivity MXScarna(seed): 0.556 RNAwolf: 0.405 Positive Predictive Value MXScarna(seed): 0.764 RNAwolf: 0.388 Number of pairs reference - predicted secondary structure: 664 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.662 Vsfold4: 0.341 Sensitivity MXScarna(seed): 0.570 Vsfold4: 0.309 Positive Predictive Value MXScarna(seed): 0.770 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 636 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.662 Vsfold5: 0.318 Sensitivity MXScarna(seed): 0.570 Vsfold5: 0.297 Positive Predictive Value MXScarna(seed): 0.770 Vsfold5: 0.343 Number of pairs reference - predicted secondary structure: 631 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.749 Alterna: 0.560 Sensitivity MXScarna(seed): 0.715 Alterna: 0.552 Positive Predictive Value MXScarna(seed): 0.788 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.749 RDfolder: 0.487 Sensitivity MXScarna(seed): 0.715 RDfolder: 0.421 Positive Predictive Value MXScarna(seed): 0.788 RDfolder: 0.571 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.665 Carnac(seed): 0.244 Sensitivity MXScarna(seed): 0.584 Carnac(seed): 0.069 Positive Predictive Value MXScarna(seed): 0.758 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.752 MCFold: 0.472 Sensitivity MXScarna(seed): 0.715 MCFold: 0.525 Positive Predictive Value MXScarna(seed): 0.793 MCFold: 0.432 Number of pairs reference - predicted secondary structure: 198 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.653 RSpredict(seed): 0.370 Sensitivity MXScarna(seed): 0.567 RSpredict(seed): 0.229 Positive Predictive Value MXScarna(seed): 0.753 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 701 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.664 NanoFolder: 0.202 Sensitivity MXScarna(seed): 0.566 NanoFolder: 0.232 Positive Predictive Value MXScarna(seed): 0.780 NanoFolder: 0.179 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.646 Mastr(seed): 0.113 Sensitivity MXScarna(seed): 0.555 Mastr(seed): 0.016 Positive Predictive Value MXScarna(seed): 0.754 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 640 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(20)	19 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 MXScarna(20): 0.840 Sensitivity TurboFold(seed): 0.851 MXScarna(20): 0.817 Positive Predictive Value TurboFold(seed): 0.867 MXScarna(20): 0.865 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.86109605532e-08	626 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 MXScarna(20): 0.644 Sensitivity PETfold_pre2.0(seed): 0.729 MXScarna(20): 0.586 Positive Predictive Value PETfold_pre2.0(seed): 0.830 MXScarna(20): 0.708 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.791 MXScarna(20): 0.647 Sensitivity ContextFold: 0.752 MXScarna(20): 0.589 Positive Predictive Value ContextFold: 0.832 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.787 MXScarna(20): 0.701 Sensitivity TurboFold(20): 0.740 MXScarna(20): 0.634 Positive Predictive Value TurboFold(20): 0.837 MXScarna(20): 0.776 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 MXScarna(20): 0.668 Sensitivity CentroidAlifold(seed): 0.652 MXScarna(20): 0.600 Positive Predictive Value CentroidAlifold(seed): 0.918 MXScarna(20): 0.744 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 MXScarna(20): 0.646 Sensitivity PETfold_pre2.0(20): 0.686 MXScarna(20): 0.589 Positive Predictive Value PETfold_pre2.0(20): 0.807 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.740 MXScarna(20): 0.647 Sensitivity CentroidAlifold(20): 0.616 MXScarna(20): 0.589 Positive Predictive Value CentroidAlifold(20): 0.891 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 MXScarna(20): 0.701 Sensitivity CentroidHomfold‑LAST: 0.625 MXScarna(20): 0.634 Positive Predictive Value CentroidHomfold‑LAST: 0.899 MXScarna(20): 0.776 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.758 MXScarna(20): 0.697 Sensitivity PPfold(20): 0.654 MXScarna(20): 0.632 Positive Predictive Value PPfold(20): 0.879 MXScarna(20): 0.770 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.687 MXScarna(20): 0.647 Sensitivity RNAalifold(20): 0.600 MXScarna(20): 0.589 Positive Predictive Value RNAalifold(20): 0.787 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	416 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.682 MXScarna(20): 0.670 Sensitivity MXScarna(seed): 0.601 MXScarna(20): 0.602 Positive Predictive Value MXScarna(seed): 0.774 MXScarna(20): 0.746 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.647 IPknot: 0.609 Sensitivity MXScarna(20): 0.589 IPknot: 0.546 Positive Predictive Value MXScarna(20): 0.710 IPknot: 0.679 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.698 Multilign(20): 0.685 Sensitivity MXScarna(20): 0.630 Multilign(20): 0.617 Positive Predictive Value MXScarna(20): 0.774 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.691 Murlet(20): 0.629 Sensitivity MXScarna(20): 0.631 Murlet(20): 0.503 Positive Predictive Value MXScarna(20): 0.757 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.661 RNAalifold(seed): 0.648 Sensitivity MXScarna(20): 0.594 RNAalifold(seed): 0.508 Positive Predictive Value MXScarna(20): 0.735 RNAalifold(seed): 0.826 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.649 CentroidFold: 0.569 Sensitivity MXScarna(20): 0.591 CentroidFold: 0.508 Positive Predictive Value MXScarna(20): 0.713 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(20): 0.748 RNASampler(20): 0.676 Sensitivity MXScarna(20): 0.705 RNASampler(20): 0.522 Positive Predictive Value MXScarna(20): 0.794 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.647 Contrafold: 0.554 Sensitivity MXScarna(20): 0.589 Contrafold: 0.536 Positive Predictive Value MXScarna(20): 0.710 Contrafold: 0.572 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.647 Sfold: 0.530 Sensitivity MXScarna(20): 0.589 Sfold: 0.475 Positive Predictive Value MXScarna(20): 0.710 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(20) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(20): 0.749 Multilign(seed): 0.334 Sensitivity MXScarna(20): 0.698 Multilign(seed): 0.186 Positive Predictive Value MXScarna(20): 0.811 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.647 MaxExpect: 0.512 Sensitivity MXScarna(20): 0.589 MaxExpect: 0.499 Positive Predictive Value MXScarna(20): 0.710 MaxExpect: 0.527 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.647 ProbKnot: 0.507 Sensitivity MXScarna(20): 0.589 ProbKnot: 0.498 Positive Predictive Value MXScarna(20): 0.710 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.647 Fold: 0.485 Sensitivity MXScarna(20): 0.589 Fold: 0.486 Positive Predictive Value MXScarna(20): 0.710 Fold: 0.485 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(20): 0.835 RNASampler(seed): 0.571 Sensitivity MXScarna(20): 0.800 RNASampler(seed): 0.343 Positive Predictive Value MXScarna(20): 0.874 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.647 UNAFold: 0.497 Sensitivity MXScarna(20): 0.589 UNAFold: 0.491 Positive Predictive Value MXScarna(20): 0.710 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.701 RNAsubopt: 0.570 Sensitivity MXScarna(20): 0.634 RNAsubopt: 0.570 Positive Predictive Value MXScarna(20): 0.776 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.647 RSpredict(20): 0.487 Sensitivity MXScarna(20): 0.589 RSpredict(20): 0.402 Positive Predictive Value MXScarna(20): 0.710 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.702 CMfinder(20): 0.549 Sensitivity MXScarna(20): 0.636 CMfinder(20): 0.380 Positive Predictive Value MXScarna(20): 0.776 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.699 PknotsRG: 0.521 Sensitivity MXScarna(20): 0.634 PknotsRG: 0.514 Positive Predictive Value MXScarna(20): 0.771 PknotsRG: 0.529 Number of pairs reference - predicted secondary structure: 611 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.647 Carnac(20): 0.518 Sensitivity MXScarna(20): 0.589 Carnac(20): 0.301 Positive Predictive Value MXScarna(20): 0.710 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.647 RNAfold: 0.482 Sensitivity MXScarna(20): 0.589 RNAfold: 0.480 Positive Predictive Value MXScarna(20): 0.710 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CMfinder(seed) Matthews Correlation Coefficient MXScarna(20): 0.820 CMfinder(seed): 0.736 Sensitivity MXScarna(20): 0.785 CMfinder(seed): 0.607 Positive Predictive Value MXScarna(20): 0.860 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.635 Afold: 0.474 Sensitivity MXScarna(20): 0.575 Afold: 0.470 Positive Predictive Value MXScarna(20): 0.702 Afold: 0.479 Number of pairs reference - predicted secondary structure: 421 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.838 HotKnots: 0.698 Sensitivity MXScarna(20): 0.791 HotKnots: 0.695 Positive Predictive Value MXScarna(20): 0.891 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.699 CRWrnafold: 0.541 Sensitivity MXScarna(20): 0.633 CRWrnafold: 0.532 Positive Predictive Value MXScarna(20): 0.772 CRWrnafold: 0.551 Number of pairs reference - predicted secondary structure: 590 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.872 Pknots: 0.655 Sensitivity MXScarna(20): 0.834 Pknots: 0.662 Positive Predictive Value MXScarna(20): 0.913 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.701 McQFold: 0.484 Sensitivity MXScarna(20): 0.634 McQFold: 0.464 Positive Predictive Value MXScarna(20): 0.776 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.701 RNAshapes: 0.526 Sensitivity MXScarna(20): 0.635 RNAshapes: 0.514 Positive Predictive Value MXScarna(20): 0.776 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.838 PPfold(seed): 0.453 Sensitivity MXScarna(20): 0.778 PPfold(seed): 0.224 Positive Predictive Value MXScarna(20): 0.904 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.89920829651e-08	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.629 Mastr(20): 0.296 Sensitivity MXScarna(20): 0.574 Mastr(20): 0.111 Positive Predictive Value MXScarna(20): 0.690 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.839 Murlet(seed): 0.631 Sensitivity MXScarna(20): 0.803 Murlet(seed): 0.418 Positive Predictive Value MXScarna(20): 0.879 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.703 RNASLOpt: 0.500 Sensitivity MXScarna(20): 0.637 RNASLOpt: 0.464 Positive Predictive Value MXScarna(20): 0.776 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.841 Cylofold: 0.557 Sensitivity MXScarna(20): 0.795 Cylofold: 0.543 Positive Predictive Value MXScarna(20): 0.892 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.701 RNAwolf: 0.414 Sensitivity MXScarna(20): 0.634 RNAwolf: 0.423 Positive Predictive Value MXScarna(20): 0.776 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.702 Vsfold4: 0.390 Sensitivity MXScarna(20): 0.635 Vsfold4: 0.356 Positive Predictive Value MXScarna(20): 0.777 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.701 Vsfold5: 0.365 Sensitivity MXScarna(20): 0.634 Vsfold5: 0.341 Positive Predictive Value MXScarna(20): 0.776 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.873 Alterna: 0.618 Sensitivity MXScarna(20): 0.835 Alterna: 0.626 Positive Predictive Value MXScarna(20): 0.915 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.873 RDfolder: 0.556 Sensitivity MXScarna(20): 0.835 RDfolder: 0.511 Positive Predictive Value MXScarna(20): 0.915 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.822 Carnac(seed): 0.398 Sensitivity MXScarna(20): 0.786 Carnac(seed): 0.173 Positive Predictive Value MXScarna(20): 0.860 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.833 MCFold: 0.500 Sensitivity MXScarna(20): 0.786 MCFold: 0.559 Positive Predictive Value MXScarna(20): 0.886 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.668 RSpredict(seed): 0.410 Sensitivity MXScarna(20): 0.600 RSpredict(seed): 0.277 Positive Predictive Value MXScarna(20): 0.744 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.683 NanoFolder: 0.189 Sensitivity MXScarna(20): 0.614 NanoFolder: 0.218 Positive Predictive Value MXScarna(20): 0.761 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.691 Mastr(seed): 0.104 Sensitivity MXScarna(20): 0.615 Mastr(seed): 0.013 Positive Predictive Value MXScarna(20): 0.778 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08
IPknot	51 TurboFold(seed) vs IPknot Matthews Correlation Coefficient TurboFold(seed): 0.791 IPknot: 0.726 Sensitivity TurboFold(seed): 0.762 IPknot: 0.705 Positive Predictive Value TurboFold(seed): 0.822 IPknot: 0.750 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1224 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 IPknot: 0.606 Sensitivity PETfold_pre2.0(seed): 0.675 IPknot: 0.549 Positive Predictive Value PETfold_pre2.0(seed): 0.814 IPknot: 0.669 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	1972 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.687 IPknot: 0.563 Sensitivity ContextFold: 0.650 IPknot: 0.501 Positive Predictive Value ContextFold: 0.727 IPknot: 0.632 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.787 IPknot: 0.688 Sensitivity TurboFold(20): 0.740 IPknot: 0.629 Positive Predictive Value TurboFold(20): 0.837 IPknot: 0.753 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 IPknot: 0.632 Sensitivity CentroidAlifold(seed): 0.623 IPknot: 0.570 Positive Predictive Value CentroidAlifold(seed): 0.901 IPknot: 0.702 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 IPknot: 0.608 Sensitivity PETfold_pre2.0(20): 0.686 IPknot: 0.545 Positive Predictive Value PETfold_pre2.0(20): 0.807 IPknot: 0.679 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.740 IPknot: 0.609 Sensitivity CentroidAlifold(20): 0.616 IPknot: 0.546 Positive Predictive Value CentroidAlifold(20): 0.891 IPknot: 0.679 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 IPknot: 0.635 Sensitivity CentroidHomfold‑LAST: 0.527 IPknot: 0.588 Positive Predictive Value CentroidHomfold‑LAST: 0.850 IPknot: 0.688 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.758 IPknot: 0.677 Sensitivity PPfold(20): 0.654 IPknot: 0.616 Positive Predictive Value PPfold(20): 0.879 IPknot: 0.746 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.687 IPknot: 0.609 Sensitivity RNAalifold(20): 0.600 IPknot: 0.546 Positive Predictive Value RNAalifold(20): 0.787 IPknot: 0.679 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	728 MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.654 IPknot: 0.633 Sensitivity MXScarna(seed): 0.568 IPknot: 0.571 Positive Predictive Value MXScarna(seed): 0.753 IPknot: 0.703 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.647 IPknot: 0.609 Sensitivity MXScarna(20): 0.589 IPknot: 0.546 Positive Predictive Value MXScarna(20): 0.710 IPknot: 0.679 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.690 Multilign(20): 0.685 Sensitivity IPknot: 0.631 Multilign(20): 0.617 Positive Predictive Value IPknot: 0.755 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.672 Murlet(20): 0.629 Sensitivity IPknot: 0.612 Murlet(20): 0.503 Positive Predictive Value IPknot: 0.738 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.634 IPknot: 0.627 Sensitivity RNAalifold(seed): 0.482 IPknot: 0.564 Positive Predictive Value RNAalifold(seed): 0.835 IPknot: 0.696 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.565 CentroidFold: 0.534 Sensitivity IPknot: 0.504 CentroidFold: 0.475 Positive Predictive Value IPknot: 0.634 CentroidFold: 0.600 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.713 RNASampler(20): 0.676 Sensitivity IPknot: 0.674 RNASampler(20): 0.522 Positive Predictive Value IPknot: 0.756 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.563 Contrafold: 0.522 Sensitivity IPknot: 0.501 Contrafold: 0.507 Positive Predictive Value IPknot: 0.632 Contrafold: 0.539 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.563 Sfold: 0.482 Sensitivity IPknot: 0.501 Sfold: 0.433 Positive Predictive Value IPknot: 0.632 Sfold: 0.536 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs IPknot Matthews Correlation Coefficient Multilign(seed): 0.681 IPknot: 0.642 Sensitivity Multilign(seed): 0.649 IPknot: 0.625 Positive Predictive Value Multilign(seed): 0.717 IPknot: 0.661 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.59469103578e-08	+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.563 MaxExpect: 0.477 Sensitivity IPknot: 0.501 MaxExpect: 0.466 Positive Predictive Value IPknot: 0.632 MaxExpect: 0.489 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.563 ProbKnot: 0.472 Sensitivity IPknot: 0.501 ProbKnot: 0.469 Positive Predictive Value IPknot: 0.632 ProbKnot: 0.476 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.563 Fold: 0.449 Sensitivity IPknot: 0.501 Fold: 0.454 Positive Predictive Value IPknot: 0.632 Fold: 0.445 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.673 RNASampler(seed): 0.629 Sensitivity IPknot: 0.620 RNASampler(seed): 0.468 Positive Predictive Value IPknot: 0.732 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.563 UNAFold: 0.447 Sensitivity IPknot: 0.501 UNAFold: 0.446 Positive Predictive Value IPknot: 0.632 UNAFold: 0.449 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.635 RNAsubopt: 0.525 Sensitivity IPknot: 0.588 RNAsubopt: 0.530 Positive Predictive Value IPknot: 0.688 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.609 RSpredict(20): 0.487 Sensitivity IPknot: 0.546 RSpredict(20): 0.402 Positive Predictive Value IPknot: 0.679 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.687 CMfinder(20): 0.549 Sensitivity IPknot: 0.628 CMfinder(20): 0.380 Positive Predictive Value IPknot: 0.752 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.587 PknotsRG: 0.466 Sensitivity IPknot: 0.525 PknotsRG: 0.467 Positive Predictive Value IPknot: 0.657 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.609 Carnac(20): 0.518 Sensitivity IPknot: 0.546 Carnac(20): 0.301 Positive Predictive Value IPknot: 0.679 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.563 RNAfold: 0.441 Sensitivity IPknot: 0.501 RNAfold: 0.444 Positive Predictive Value IPknot: 0.632 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.700 CMfinder(seed): 0.486 Sensitivity IPknot: 0.661 CMfinder(seed): 0.312 Positive Predictive Value IPknot: 0.742 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.556 Afold: 0.434 Sensitivity IPknot: 0.490 Afold: 0.434 Positive Predictive Value IPknot: 0.632 Afold: 0.435 Number of pairs reference - predicted secondary structure: 1274 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.692 HotKnots: 0.613 Sensitivity IPknot: 0.659 HotKnots: 0.607 Positive Predictive Value IPknot: 0.730 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.587 CRWrnafold: 0.437 Sensitivity IPknot: 0.526 CRWrnafold: 0.440 Positive Predictive Value IPknot: 0.655 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.687 Pknots: 0.606 Sensitivity IPknot: 0.652 Pknots: 0.595 Positive Predictive Value IPknot: 0.729 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.626 McQFold: 0.467 Sensitivity IPknot: 0.577 McQFold: 0.457 Positive Predictive Value IPknot: 0.679 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.637 RNAshapes: 0.477 Sensitivity IPknot: 0.589 RNAshapes: 0.472 Positive Predictive Value IPknot: 0.691 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.725 PPfold(seed): 0.626 Sensitivity IPknot: 0.708 PPfold(seed): 0.495 Positive Predictive Value IPknot: 0.744 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.604 Mastr(20): 0.296 Sensitivity IPknot: 0.546 Mastr(20): 0.111 Positive Predictive Value IPknot: 0.668 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.680 Murlet(seed): 0.540 Sensitivity IPknot: 0.639 Murlet(seed): 0.360 Positive Predictive Value IPknot: 0.725 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.639 RNASLOpt: 0.470 Sensitivity IPknot: 0.591 RNASLOpt: 0.442 Positive Predictive Value IPknot: 0.691 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.718 Cylofold: 0.575 Sensitivity IPknot: 0.686 Cylofold: 0.551 Positive Predictive Value IPknot: 0.757 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.599 RNAwolf: 0.343 Sensitivity IPknot: 0.542 RNAwolf: 0.358 Positive Predictive Value IPknot: 0.663 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.636 Vsfold4: 0.346 Sensitivity IPknot: 0.588 Vsfold4: 0.318 Positive Predictive Value IPknot: 0.688 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.636 Vsfold5: 0.339 Sensitivity IPknot: 0.589 Vsfold5: 0.322 Positive Predictive Value IPknot: 0.689 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.689 Alterna: 0.552 Sensitivity IPknot: 0.655 Alterna: 0.547 Positive Predictive Value IPknot: 0.731 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.689 RDfolder: 0.520 Sensitivity IPknot: 0.655 RDfolder: 0.464 Positive Predictive Value IPknot: 0.731 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.644 Carnac(seed): 0.244 Sensitivity IPknot: 0.613 Carnac(seed): 0.069 Positive Predictive Value IPknot: 0.677 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.689 MCFold: 0.473 Sensitivity IPknot: 0.654 MCFold: 0.524 Positive Predictive Value IPknot: 0.730 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.632 RSpredict(seed): 0.369 Sensitivity IPknot: 0.571 RSpredict(seed): 0.229 Positive Predictive Value IPknot: 0.700 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.671 NanoFolder: 0.194 Sensitivity IPknot: 0.616 NanoFolder: 0.229 Positive Predictive Value IPknot: 0.731 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.658 Mastr(seed): 0.113 Sensitivity IPknot: 0.606 Mastr(seed): 0.016 Positive Predictive Value IPknot: 0.714 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08
Multilign(20)	18 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.854 Multilign(20): 0.589 Sensitivity TurboFold(seed): 0.846 Multilign(20): 0.433 Positive Predictive Value TurboFold(seed): 0.864 Multilign(20): 0.806 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	519 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.800 Multilign(20): 0.689 Sensitivity PETfold_pre2.0(seed): 0.728 Multilign(20): 0.623 Positive Predictive Value PETfold_pre2.0(seed): 0.879 Multilign(20): 0.764 Number of pairs reference - predicted secondary structure: 519 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.866 Multilign(20): 0.685 Sensitivity ContextFold: 0.827 Multilign(20): 0.617 Positive Predictive Value ContextFold: 0.908 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.786 Multilign(20): 0.685 Sensitivity TurboFold(20): 0.739 Multilign(20): 0.617 Positive Predictive Value TurboFold(20): 0.837 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.740 Multilign(20): 0.650 Sensitivity CentroidAlifold(seed): 0.580 Multilign(20): 0.573 Positive Predictive Value CentroidAlifold(seed): 0.945 Multilign(20): 0.738 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	531 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.768 Multilign(20): 0.685 Sensitivity PETfold_pre2.0(20): 0.677 Multilign(20): 0.618 Positive Predictive Value PETfold_pre2.0(20): 0.871 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 531 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.758 Multilign(20): 0.685 Sensitivity CentroidAlifold(20): 0.619 Multilign(20): 0.617 Positive Predictive Value CentroidAlifold(20): 0.929 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.747 Multilign(20): 0.685 Sensitivity CentroidHomfold‑LAST: 0.622 Multilign(20): 0.617 Positive Predictive Value CentroidHomfold‑LAST: 0.898 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	522 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.763 Multilign(20): 0.687 Sensitivity PPfold(20): 0.656 Multilign(20): 0.620 Positive Predictive Value PPfold(20): 0.888 Multilign(20): 0.763 Number of pairs reference - predicted secondary structure: 522 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.707 Multilign(20): 0.685 Sensitivity RNAalifold(20): 0.578 Multilign(20): 0.617 Positive Predictive Value RNAalifold(20): 0.866 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	330 MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.697 Multilign(20): 0.653 Sensitivity MXScarna(seed): 0.600 Multilign(20): 0.577 Positive Predictive Value MXScarna(seed): 0.810 Multilign(20): 0.741 Number of pairs reference - predicted secondary structure: 330 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.698 Multilign(20): 0.685 Sensitivity MXScarna(20): 0.630 Multilign(20): 0.617 Positive Predictive Value MXScarna(20): 0.774 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.690 Multilign(20): 0.685 Sensitivity IPknot: 0.631 Multilign(20): 0.617 Positive Predictive Value IPknot: 0.755 Multilign(20): 0.762 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 4.48494289621e-08		+ Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.701 Murlet(20): 0.632 Sensitivity Multilign(20): 0.634 Murlet(20): 0.499 Positive Predictive Value Multilign(20): 0.776 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 465 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(20): 0.649 RNAalifold(seed): 0.494 Sensitivity Multilign(20): 0.572 RNAalifold(seed): 0.289 Positive Predictive Value Multilign(20): 0.737 RNAalifold(seed): 0.846 Number of pairs reference - predicted secondary structure: 312 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.685 CentroidFold: 0.655 Sensitivity Multilign(20): 0.617 CentroidFold: 0.598 Positive Predictive Value Multilign(20): 0.762 CentroidFold: 0.718 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.712 RNASampler(20): 0.685 Sensitivity Multilign(20): 0.639 RNASampler(20): 0.533 Positive Predictive Value Multilign(20): 0.795 RNASampler(20): 0.881 Number of pairs reference - predicted secondary structure: 372 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.685 Contrafold: 0.642 Sensitivity Multilign(20): 0.617 Contrafold: 0.624 Positive Predictive Value Multilign(20): 0.762 Contrafold: 0.662 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.685 Sfold: 0.614 Sensitivity Multilign(20): 0.617 Sfold: 0.557 Positive Predictive Value Multilign(20): 0.762 Sfold: 0.678 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(20) vs Multilign(seed) Matthews Correlation Coefficient Multilign(20): 0.588 Multilign(seed): 0.334 Sensitivity Multilign(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value Multilign(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.685 MaxExpect: 0.624 Sensitivity Multilign(20): 0.617 MaxExpect: 0.604 Positive Predictive Value Multilign(20): 0.762 MaxExpect: 0.647 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.685 ProbKnot: 0.622 Sensitivity Multilign(20): 0.617 ProbKnot: 0.606 Positive Predictive Value Multilign(20): 0.762 ProbKnot: 0.640 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.685 Fold: 0.601 Sensitivity Multilign(20): 0.617 Fold: 0.595 Positive Predictive Value Multilign(20): 0.762 Fold: 0.610 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(20): 0.692 RNASampler(seed): 0.571 Sensitivity Multilign(20): 0.552 RNASampler(seed): 0.343 Positive Predictive Value Multilign(20): 0.874 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.685 UNAFold: 0.591 Sensitivity Multilign(20): 0.617 UNAFold: 0.579 Positive Predictive Value Multilign(20): 0.762 UNAFold: 0.605 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.685 RNAsubopt: 0.571 Sensitivity Multilign(20): 0.617 RNAsubopt: 0.570 Positive Predictive Value Multilign(20): 0.762 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.685 RSpredict(20): 0.514 Sensitivity Multilign(20): 0.617 RSpredict(20): 0.374 Positive Predictive Value Multilign(20): 0.762 RSpredict(20): 0.708 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.686 CMfinder(20): 0.554 Sensitivity Multilign(20): 0.619 CMfinder(20): 0.385 Positive Predictive Value Multilign(20): 0.762 CMfinder(20): 0.799 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.685 PknotsRG: 0.567 Sensitivity Multilign(20): 0.617 PknotsRG: 0.560 Positive Predictive Value Multilign(20): 0.762 PknotsRG: 0.576 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.685 Carnac(20): 0.467 Sensitivity Multilign(20): 0.617 Carnac(20): 0.245 Positive Predictive Value Multilign(20): 0.762 Carnac(20): 0.891 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.685 RNAfold: 0.580 Sensitivity Multilign(20): 0.617 RNAfold: 0.573 Positive Predictive Value Multilign(20): 0.762 RNAfold: 0.589 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Multilign(20): 0.657 Sensitivity CMfinder(seed): 0.607 Multilign(20): 0.508 Positive Predictive Value CMfinder(seed): 0.898 Multilign(20): 0.856 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.666 Afold: 0.573 Sensitivity Multilign(20): 0.594 Afold: 0.560 Positive Predictive Value Multilign(20): 0.749 Afold: 0.587 Number of pairs reference - predicted secondary structure: 327 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs HotKnots Matthews Correlation Coefficient Multilign(20): 0.784 HotKnots: 0.696 Sensitivity Multilign(20): 0.697 HotKnots: 0.692 Positive Predictive Value Multilign(20): 0.885 HotKnots: 0.703 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.685 CRWrnafold: 0.546 Sensitivity Multilign(20): 0.617 CRWrnafold: 0.537 Positive Predictive Value Multilign(20): 0.762 CRWrnafold: 0.557 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.827 Pknots: 0.656 Sensitivity Multilign(20): 0.757 Pknots: 0.662 Positive Predictive Value Multilign(20): 0.906 Pknots: 0.654 Number of pairs reference - predicted secondary structure: 210 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.685 McQFold: 0.485 Sensitivity Multilign(20): 0.617 McQFold: 0.465 Positive Predictive Value Multilign(20): 0.762 McQFold: 0.509 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.687 RNAshapes: 0.526 Sensitivity Multilign(20): 0.619 RNAshapes: 0.514 Positive Predictive Value Multilign(20): 0.763 RNAshapes: 0.540 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.611 PPfold(seed): 0.354 Sensitivity Multilign(20): 0.462 PPfold(seed): 0.136 Positive Predictive Value Multilign(20): 0.811 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.685 Mastr(20): 0.360 Sensitivity Multilign(20): 0.617 Mastr(20): 0.165 Positive Predictive Value Multilign(20): 0.762 Mastr(20): 0.788 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Murlet(seed) Matthews Correlation Coefficient Multilign(20): 0.673 Murlet(seed): 0.636 Sensitivity Multilign(20): 0.523 Murlet(seed): 0.428 Positive Predictive Value Multilign(20): 0.872 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.690 RNASLOpt: 0.506 Sensitivity Multilign(20): 0.623 RNASLOpt: 0.469 Positive Predictive Value Multilign(20): 0.765 RNASLOpt: 0.548 Number of pairs reference - predicted secondary structure: 520 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Cylofold Matthews Correlation Coefficient Multilign(20): 0.783 Cylofold: 0.563 Sensitivity Multilign(20): 0.695 Cylofold: 0.549 Positive Predictive Value Multilign(20): 0.884 Cylofold: 0.583 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.685 RNAwolf: 0.416 Sensitivity Multilign(20): 0.617 RNAwolf: 0.425 Positive Predictive Value Multilign(20): 0.762 RNAwolf: 0.410 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.685 Vsfold4: 0.400 Sensitivity Multilign(20): 0.617 Vsfold4: 0.364 Positive Predictive Value Multilign(20): 0.761 Vsfold4: 0.441 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.686 Vsfold5: 0.377 Sensitivity Multilign(20): 0.618 Vsfold5: 0.351 Positive Predictive Value Multilign(20): 0.762 Vsfold5: 0.407 Number of pairs reference - predicted secondary structure: 527 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.829 Alterna: 0.616 Sensitivity Multilign(20): 0.758 Alterna: 0.624 Positive Predictive Value Multilign(20): 0.910 Alterna: 0.614 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.829 RDfolder: 0.561 Sensitivity Multilign(20): 0.758 RDfolder: 0.517 Positive Predictive Value Multilign(20): 0.910 RDfolder: 0.616 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.678 Carnac(seed): 0.357 Sensitivity Multilign(20): 0.562 Carnac(seed): 0.141 Positive Predictive Value Multilign(20): 0.820 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.774 MCFold: 0.498 Sensitivity Multilign(20): 0.681 MCFold: 0.558 Positive Predictive Value Multilign(20): 0.883 MCFold: 0.451 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.650 RSpredict(seed): 0.233 Sensitivity Multilign(20): 0.574 RSpredict(seed): 0.099 Positive Predictive Value Multilign(20): 0.737 RSpredict(seed): 0.548 Number of pairs reference - predicted secondary structure: 318 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.659 NanoFolder: 0.193 Sensitivity Multilign(20): 0.586 NanoFolder: 0.222 Positive Predictive Value Multilign(20): 0.743 NanoFolder: 0.171 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.654 Mastr(seed): 0.112 Sensitivity Multilign(20): 0.578 Mastr(seed): 0.015 Positive Predictive Value Multilign(20): 0.742 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(20)	17 TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.902 Murlet(20): 0.628 Sensitivity TurboFold(seed): 0.892 Murlet(20): 0.414 Positive Predictive Value TurboFold(seed): 0.914 Murlet(20): 0.957 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	499 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.801 Murlet(20): 0.630 Sensitivity PETfold_pre2.0(seed): 0.738 Murlet(20): 0.505 Positive Predictive Value PETfold_pre2.0(seed): 0.869 Murlet(20): 0.786 Number of pairs reference - predicted secondary structure: 499 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.843 Murlet(20): 0.629 Sensitivity ContextFold: 0.804 Murlet(20): 0.503 Positive Predictive Value ContextFold: 0.885 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	495 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.793 Murlet(20): 0.631 Sensitivity TurboFold(20): 0.747 Murlet(20): 0.496 Positive Predictive Value TurboFold(20): 0.842 Murlet(20): 0.803 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	285 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.763 Murlet(20): 0.589 Sensitivity CentroidAlifold(seed): 0.627 Murlet(20): 0.450 Positive Predictive Value CentroidAlifold(seed): 0.930 Murlet(20): 0.770 Number of pairs reference - predicted secondary structure: 285 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 Murlet(20): 0.629 Sensitivity PETfold_pre2.0(20): 0.686 Murlet(20): 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.855 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 Murlet(20): 0.629 Sensitivity CentroidAlifold(20): 0.638 Murlet(20): 0.503 Positive Predictive Value CentroidAlifold(20): 0.915 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	495 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.761 Murlet(20): 0.631 Sensitivity CentroidHomfold‑LAST: 0.648 Murlet(20): 0.496 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Murlet(20): 0.803 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	487 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.767 Murlet(20): 0.634 Sensitivity PPfold(20): 0.664 Murlet(20): 0.500 Positive Predictive Value PPfold(20): 0.888 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 487 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.714 Murlet(20): 0.629 Sensitivity RNAalifold(20): 0.603 Murlet(20): 0.503 Positive Predictive Value RNAalifold(20): 0.846 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	297 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.702 Murlet(20): 0.592 Sensitivity MXScarna(seed): 0.620 Murlet(20): 0.454 Positive Predictive Value MXScarna(seed): 0.794 Murlet(20): 0.773 Number of pairs reference - predicted secondary structure: 297 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.691 Murlet(20): 0.629 Sensitivity MXScarna(20): 0.631 Murlet(20): 0.503 Positive Predictive Value MXScarna(20): 0.757 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.672 Murlet(20): 0.629 Sensitivity IPknot: 0.612 Murlet(20): 0.503 Positive Predictive Value IPknot: 0.738 Murlet(20): 0.787 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	465 Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.701 Murlet(20): 0.632 Sensitivity Multilign(20): 0.634 Murlet(20): 0.499 Positive Predictive Value Multilign(20): 0.776 Murlet(20): 0.804 Number of pairs reference - predicted secondary structure: 465 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Murlet(20) vs RNAalifold(seed) Matthews Correlation Coefficient Murlet(20): 0.587 RNAalifold(seed): 0.572 Sensitivity Murlet(20): 0.449 RNAalifold(seed): 0.386 Positive Predictive Value Murlet(20): 0.770 RNAalifold(seed): 0.848 Number of pairs reference - predicted secondary structure: 281 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Murlet(20) vs CentroidFold Matthews Correlation Coefficient Murlet(20): 0.629 CentroidFold: 0.627 Sensitivity Murlet(20): 0.503 CentroidFold: 0.569 Positive Predictive Value Murlet(20): 0.787 CentroidFold: 0.692 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 0.00610617588669	+ Murlet(20) vs RNASampler(20) Matthews Correlation Coefficient Murlet(20): 0.694 RNASampler(20): 0.689 Sensitivity Murlet(20): 0.574 RNASampler(20): 0.541 Positive Predictive Value Murlet(20): 0.841 RNASampler(20): 0.878 Number of pairs reference - predicted secondary structure: 383 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.629 Contrafold: 0.613 Sensitivity Murlet(20): 0.503 Contrafold: 0.595 Positive Predictive Value Murlet(20): 0.787 Contrafold: 0.632 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.629 Sfold: 0.591 Sensitivity Murlet(20): 0.503 Sfold: 0.532 Positive Predictive Value Murlet(20): 0.787 Sfold: 0.657 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): 0.568 Multilign(seed): 0.334 Sensitivity Murlet(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value Murlet(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs MaxExpect Matthews Correlation Coefficient Murlet(20): 0.629 MaxExpect: 0.591 Sensitivity Murlet(20): 0.503 MaxExpect: 0.574 Positive Predictive Value Murlet(20): 0.787 MaxExpect: 0.610 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs ProbKnot Matthews Correlation Coefficient Murlet(20): 0.629 ProbKnot: 0.588 Sensitivity Murlet(20): 0.503 ProbKnot: 0.576 Positive Predictive Value Murlet(20): 0.787 ProbKnot: 0.601 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.629 Fold: 0.571 Sensitivity Murlet(20): 0.503 Fold: 0.568 Positive Predictive Value Murlet(20): 0.787 Fold: 0.576 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNASampler(seed) Matthews Correlation Coefficient Murlet(20): 0.685 RNASampler(seed): 0.571 Sensitivity Murlet(20): 0.527 RNASampler(seed): 0.343 Positive Predictive Value Murlet(20): 0.896 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.629 UNAFold: 0.563 Sensitivity Murlet(20): 0.503 UNAFold: 0.554 Positive Predictive Value Murlet(20): 0.787 UNAFold: 0.573 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.631 RNAsubopt: 0.573 Sensitivity Murlet(20): 0.496 RNAsubopt: 0.573 Positive Predictive Value Murlet(20): 0.803 RNAsubopt: 0.575 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.629 RSpredict(20): 0.552 Sensitivity Murlet(20): 0.503 RSpredict(20): 0.436 Positive Predictive Value Murlet(20): 0.787 RSpredict(20): 0.700 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.631 CMfinder(20): 0.560 Sensitivity Murlet(20): 0.498 CMfinder(20): 0.394 Positive Predictive Value Murlet(20): 0.803 CMfinder(20): 0.797 Number of pairs reference - predicted secondary structure: 491 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.644 PknotsRG: 0.556 Sensitivity Murlet(20): 0.514 PknotsRG: 0.551 Positive Predictive Value Murlet(20): 0.808 PknotsRG: 0.563 Number of pairs reference - predicted secondary structure: 501 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.629 Carnac(20): 0.512 Sensitivity Murlet(20): 0.503 Carnac(20): 0.296 Positive Predictive Value Murlet(20): 0.787 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.629 RNAfold: 0.553 Sensitivity Murlet(20): 0.503 RNAfold: 0.548 Positive Predictive Value Murlet(20): 0.787 RNAfold: 0.559 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs Murlet(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Murlet(20): 0.649 Sensitivity CMfinder(seed): 0.607 Murlet(20): 0.483 Positive Predictive Value CMfinder(seed): 0.898 Murlet(20): 0.878 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.598 Afold: 0.537 Sensitivity Murlet(20): 0.466 Afold: 0.528 Positive Predictive Value Murlet(20): 0.769 Afold: 0.548 Number of pairs reference - predicted secondary structure: 292 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.750 HotKnots: 0.699 Sensitivity Murlet(20): 0.619 HotKnots: 0.696 Positive Predictive Value Murlet(20): 0.913 HotKnots: 0.706 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.638 CRWrnafold: 0.546 Sensitivity Murlet(20): 0.506 CRWrnafold: 0.538 Positive Predictive Value Murlet(20): 0.806 CRWrnafold: 0.556 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.780 Pknots: 0.657 Sensitivity Murlet(20): 0.685 Pknots: 0.663 Positive Predictive Value Murlet(20): 0.892 Pknots: 0.655 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.631 McQFold: 0.485 Sensitivity Murlet(20): 0.496 McQFold: 0.466 Positive Predictive Value Murlet(20): 0.803 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.636 RNAshapes: 0.526 Sensitivity Murlet(20): 0.501 RNAshapes: 0.515 Positive Predictive Value Murlet(20): 0.808 RNAshapes: 0.539 Number of pairs reference - predicted secondary structure: 489 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.646 PPfold(seed): 0.463 Sensitivity Murlet(20): 0.453 PPfold(seed): 0.233 Positive Predictive Value Murlet(20): 0.923 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.620 Mastr(20): 0.389 Sensitivity Murlet(20): 0.488 Mastr(20): 0.191 Positive Predictive Value Murlet(20): 0.789 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 497 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.678 Murlet(seed): 0.631 Sensitivity Murlet(20): 0.513 Murlet(seed): 0.418 Positive Predictive Value Murlet(20): 0.899 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.640 RNASLOpt: 0.497 Sensitivity Murlet(20): 0.508 RNASLOpt: 0.462 Positive Predictive Value Murlet(20): 0.809 RNASLOpt: 0.538 Number of pairs reference - predicted secondary structure: 481 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.751 Cylofold: 0.558 Sensitivity Murlet(20): 0.620 Cylofold: 0.544 Positive Predictive Value Murlet(20): 0.913 Cylofold: 0.578 Number of pairs reference - predicted secondary structure: 303 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.631 RNAwolf: 0.417 Sensitivity Murlet(20): 0.496 RNAwolf: 0.428 Positive Predictive Value Murlet(20): 0.803 RNAwolf: 0.410 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.634 Vsfold4: 0.391 Sensitivity Murlet(20): 0.500 Vsfold4: 0.357 Positive Predictive Value Murlet(20): 0.805 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 491 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.636 Vsfold5: 0.363 Sensitivity Murlet(20): 0.502 Vsfold5: 0.340 Positive Predictive Value Murlet(20): 0.807 Vsfold5: 0.390 Number of pairs reference - predicted secondary structure: 489 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.780 Alterna: 0.618 Sensitivity Murlet(20): 0.685 Alterna: 0.626 Positive Predictive Value Murlet(20): 0.892 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.780 RDfolder: 0.556 Sensitivity Murlet(20): 0.685 RDfolder: 0.511 Positive Predictive Value Murlet(20): 0.892 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.640 Carnac(seed): 0.317 Sensitivity Murlet(20): 0.488 Carnac(seed): 0.111 Positive Predictive Value Murlet(20): 0.843 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 79 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.748 MCFold: 0.501 Sensitivity Murlet(20): 0.616 MCFold: 0.560 Positive Predictive Value Murlet(20): 0.911 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 257 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.585 RSpredict(seed): 0.300 Sensitivity Murlet(20): 0.446 RSpredict(seed): 0.161 Positive Predictive Value Murlet(20): 0.769 RSpredict(seed): 0.560 Number of pairs reference - predicted secondary structure: 284 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.591 NanoFolder: 0.197 Sensitivity Murlet(20): 0.450 NanoFolder: 0.227 Positive Predictive Value Murlet(20): 0.778 NanoFolder: 0.174 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.585 Mastr(seed): 0.125 Sensitivity Murlet(20): 0.434 Mastr(seed): 0.019 Positive Predictive Value Murlet(20): 0.791 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(seed)	50 TurboFold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.788 RNAalifold(seed): 0.688 Sensitivity TurboFold(seed): 0.760 RNAalifold(seed): 0.533 Positive Predictive Value TurboFold(seed): 0.819 RNAalifold(seed): 0.888 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	682 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.760 RNAalifold(seed): 0.636 Sensitivity PETfold_pre2.0(seed): 0.697 RNAalifold(seed): 0.485 Positive Predictive Value PETfold_pre2.0(seed): 0.829 RNAalifold(seed): 0.834 Number of pairs reference - predicted secondary structure: 682 Wilcoxon single-rank test P-value: 3.56938820447e-08	700 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.803 RNAalifold(seed): 0.634 Sensitivity ContextFold: 0.765 RNAalifold(seed): 0.482 Positive Predictive Value ContextFold: 0.843 RNAalifold(seed): 0.835 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	340 TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.779 RNAalifold(seed): 0.508 Sensitivity TurboFold(20): 0.731 RNAalifold(seed): 0.302 Positive Predictive Value TurboFold(20): 0.831 RNAalifold(seed): 0.854 Number of pairs reference - predicted secondary structure: 340 Wilcoxon single-rank test P-value: 3.56938820447e-08	695 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.750 RNAalifold(seed): 0.640 Sensitivity CentroidAlifold(seed): 0.624 RNAalifold(seed): 0.486 Positive Predictive Value CentroidAlifold(seed): 0.901 RNAalifold(seed): 0.844 Number of pairs reference - predicted secondary structure: 695 Wilcoxon single-rank test P-value: 3.56938820447e-08	399 PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.757 RNAalifold(seed): 0.648 Sensitivity PETfold_pre2.0(20): 0.695 RNAalifold(seed): 0.508 Positive Predictive Value PETfold_pre2.0(20): 0.825 RNAalifold(seed): 0.826 Number of pairs reference - predicted secondary structure: 399 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.753 RNAalifold(seed): 0.648 Sensitivity CentroidAlifold(20): 0.628 RNAalifold(seed): 0.508 Positive Predictive Value CentroidAlifold(20): 0.904 RNAalifold(seed): 0.826 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	619 CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.698 RNAalifold(seed): 0.549 Sensitivity CentroidHomfold‑LAST: 0.559 RNAalifold(seed): 0.352 Positive Predictive Value CentroidHomfold‑LAST: 0.872 RNAalifold(seed): 0.859 Number of pairs reference - predicted secondary structure: 619 Wilcoxon single-rank test P-value: 3.56938820447e-08	333 PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.733 RNAalifold(seed): 0.533 Sensitivity PPfold(20): 0.621 RNAalifold(seed): 0.339 Positive Predictive Value PPfold(20): 0.865 RNAalifold(seed): 0.839 Number of pairs reference - predicted secondary structure: 333 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.704 RNAalifold(seed): 0.648 Sensitivity RNAalifold(20): 0.611 RNAalifold(seed): 0.508 Positive Predictive Value RNAalifold(20): 0.812 RNAalifold(seed): 0.826 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	696 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.652 RNAalifold(seed): 0.640 Sensitivity MXScarna(seed): 0.566 RNAalifold(seed): 0.485 Positive Predictive Value MXScarna(seed): 0.752 RNAalifold(seed): 0.844 Number of pairs reference - predicted secondary structure: 696 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.661 RNAalifold(seed): 0.648 Sensitivity MXScarna(20): 0.594 RNAalifold(seed): 0.508 Positive Predictive Value MXScarna(20): 0.735 RNAalifold(seed): 0.826 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	700 RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.634 IPknot: 0.627 Sensitivity RNAalifold(seed): 0.482 IPknot: 0.564 Positive Predictive Value RNAalifold(seed): 0.835 IPknot: 0.696 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 4.1569883686e-08	312 Multilign(20) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(20): 0.649 RNAalifold(seed): 0.494 Sensitivity Multilign(20): 0.572 RNAalifold(seed): 0.289 Positive Predictive Value Multilign(20): 0.737 RNAalifold(seed): 0.846 Number of pairs reference - predicted secondary structure: 312 Wilcoxon single-rank test P-value: 3.56938820447e-08	281 Murlet(20) vs RNAalifold(seed) Matthews Correlation Coefficient Murlet(20): 0.587 RNAalifold(seed): 0.572 Sensitivity Murlet(20): 0.449 RNAalifold(seed): 0.386 Positive Predictive Value Murlet(20): 0.770 RNAalifold(seed): 0.848 Number of pairs reference - predicted secondary structure: 281 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAalifold(seed) vs CentroidFold Matthews Correlation Coefficient RNAalifold(seed): 0.636 CentroidFold: 0.594 Sensitivity RNAalifold(seed): 0.483 CentroidFold: 0.533 Positive Predictive Value RNAalifold(seed): 0.837 CentroidFold: 0.662 Number of pairs reference - predicted secondary structure: 699 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.624 RNASampler(20): 0.584 Sensitivity RNAalifold(seed): 0.413 RNASampler(20): 0.381 Positive Predictive Value RNAalifold(seed): 0.944 RNASampler(20): 0.896 Number of pairs reference - predicted secondary structure: 174 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.634 Contrafold: 0.579 Sensitivity RNAalifold(seed): 0.482 Contrafold: 0.560 Positive Predictive Value RNAalifold(seed): 0.835 Contrafold: 0.598 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.634 Sfold: 0.565 Sensitivity RNAalifold(seed): 0.482 Sfold: 0.509 Positive Predictive Value RNAalifold(seed): 0.835 Sfold: 0.627 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.747 Multilign(seed): 0.698 Sensitivity RNAalifold(seed): 0.633 Multilign(seed): 0.660 Positive Predictive Value RNAalifold(seed): 0.883 Multilign(seed): 0.741 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.634 MaxExpect: 0.538 Sensitivity RNAalifold(seed): 0.482 MaxExpect: 0.523 Positive Predictive Value RNAalifold(seed): 0.835 MaxExpect: 0.553 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.634 ProbKnot: 0.534 Sensitivity RNAalifold(seed): 0.482 ProbKnot: 0.524 Positive Predictive Value RNAalifold(seed): 0.835 ProbKnot: 0.545 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.634 Fold: 0.513 Sensitivity RNAalifold(seed): 0.482 Fold: 0.512 Positive Predictive Value RNAalifold(seed): 0.835 Fold: 0.515 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.736 RNASampler(seed): 0.629 Sensitivity RNAalifold(seed): 0.594 RNASampler(seed): 0.468 Positive Predictive Value RNAalifold(seed): 0.913 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.634 UNAFold: 0.531 Sensitivity RNAalifold(seed): 0.482 UNAFold: 0.523 Positive Predictive Value RNAalifold(seed): 0.835 UNAFold: 0.540 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAsubopt vs RNAalifold(seed) Matthews Correlation Coefficient RNAsubopt: 0.569 RNAalifold(seed): 0.549 Sensitivity RNAsubopt: 0.570 RNAalifold(seed): 0.352 Positive Predictive Value RNAsubopt: 0.570 RNAalifold(seed): 0.859 Number of pairs reference - predicted secondary structure: 619 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.648 RSpredict(20): 0.513 Sensitivity RNAalifold(seed): 0.508 RSpredict(20): 0.412 Positive Predictive Value RNAalifold(seed): 0.826 RSpredict(20): 0.639 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.518 RNAalifold(seed): 0.508 Sensitivity CMfinder(20): 0.348 RNAalifold(seed): 0.303 Positive Predictive Value CMfinder(20): 0.772 RNAalifold(seed): 0.854 Number of pairs reference - predicted secondary structure: 336 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs PknotsRG Matthews Correlation Coefficient RNAalifold(seed): 0.652 PknotsRG: 0.529 Sensitivity RNAalifold(seed): 0.490 PknotsRG: 0.523 Positive Predictive Value RNAalifold(seed): 0.869 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 684 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.648 Carnac(20): 0.502 Sensitivity RNAalifold(seed): 0.508 Carnac(20): 0.280 Positive Predictive Value RNAalifold(seed): 0.826 Carnac(20): 0.902 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.634 RNAfold: 0.515 Sensitivity RNAalifold(seed): 0.482 RNAfold: 0.511 Positive Predictive Value RNAalifold(seed): 0.835 RNAfold: 0.520 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.693 CMfinder(seed): 0.486 Sensitivity RNAalifold(seed): 0.532 CMfinder(seed): 0.312 Positive Predictive Value RNAalifold(seed): 0.904 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Afold Matthews Correlation Coefficient RNAalifold(seed): 0.640 Afold: 0.509 Sensitivity RNAalifold(seed): 0.491 Afold: 0.503 Positive Predictive Value RNAalifold(seed): 0.835 Afold: 0.516 Number of pairs reference - predicted secondary structure: 580 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: 0.695 RNAalifold(seed): 0.605 Sensitivity HotKnots: 0.694 RNAalifold(seed): 0.399 Positive Predictive Value HotKnots: 0.701 RNAalifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.620 CRWrnafold: 0.507 Sensitivity RNAalifold(seed): 0.444 CRWrnafold: 0.502 Positive Predictive Value RNAalifold(seed): 0.868 CRWrnafold: 0.514 Number of pairs reference - predicted secondary structure: 661 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.618 Pknots: 0.488 Sensitivity RNAalifold(seed): 0.420 Pknots: 0.481 Positive Predictive Value RNAalifold(seed): 0.914 Pknots: 0.503 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.548 McQFold: 0.474 Sensitivity RNAalifold(seed): 0.350 McQFold: 0.456 Positive Predictive Value RNAalifold(seed): 0.859 McQFold: 0.494 Number of pairs reference - predicted secondary structure: 632 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.549 RNAshapes: 0.527 Sensitivity RNAalifold(seed): 0.351 RNAshapes: 0.516 Positive Predictive Value RNAalifold(seed): 0.858 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 594 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.669 PPfold(seed): 0.648 Sensitivity RNAalifold(seed): 0.521 PPfold(seed): 0.530 Positive Predictive Value RNAalifold(seed): 0.860 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.490 Mastr(20): 0.213 Sensitivity RNAalifold(seed): 0.318 Mastr(20): 0.055 Positive Predictive Value RNAalifold(seed): 0.755 Mastr(20): 0.822 Number of pairs reference - predicted secondary structure: 352 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.725 Murlet(seed): 0.540 Sensitivity RNAalifold(seed): 0.592 Murlet(seed): 0.360 Positive Predictive Value RNAalifold(seed): 0.890 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.558 RNASLOpt: 0.477 Sensitivity RNAalifold(seed): 0.361 RNASLOpt: 0.444 Positive Predictive Value RNAalifold(seed): 0.863 RNASLOpt: 0.515 Number of pairs reference - predicted secondary structure: 571 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Cylofold Matthews Correlation Coefficient RNAalifold(seed): 0.578 Cylofold: 0.512 Sensitivity RNAalifold(seed): 0.370 Cylofold: 0.484 Positive Predictive Value RNAalifold(seed): 0.909 Cylofold: 0.548 Number of pairs reference - predicted secondary structure: 187 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.548 RNAwolf: 0.394 Sensitivity RNAalifold(seed): 0.350 RNAwolf: 0.404 Positive Predictive Value RNAalifold(seed): 0.859 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 632 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.551 Vsfold4: 0.336 Sensitivity RNAalifold(seed): 0.354 Vsfold4: 0.305 Positive Predictive Value RNAalifold(seed): 0.859 Vsfold4: 0.373 Number of pairs reference - predicted secondary structure: 604 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.550 Vsfold5: 0.312 Sensitivity RNAalifold(seed): 0.353 Vsfold5: 0.291 Positive Predictive Value RNAalifold(seed): 0.859 Vsfold5: 0.338 Number of pairs reference - predicted secondary structure: 599 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): 0.617 Alterna: 0.554 Sensitivity RNAalifold(seed): 0.418 Alterna: 0.541 Positive Predictive Value RNAalifold(seed): 0.917 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.617 RDfolder: 0.448 Sensitivity RNAalifold(seed): 0.418 RDfolder: 0.382 Positive Predictive Value RNAalifold(seed): 0.917 RDfolder: 0.533 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.662 Carnac(seed): 0.246 Sensitivity RNAalifold(seed): 0.490 Carnac(seed): 0.070 Positive Predictive Value RNAalifold(seed): 0.896 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.612 MCFold: 0.476 Sensitivity RNAalifold(seed): 0.404 MCFold: 0.525 Positive Predictive Value RNAalifold(seed): 0.932 MCFold: 0.438 Number of pairs reference - predicted secondary structure: 175 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.634 RSpredict(seed): 0.371 Sensitivity RNAalifold(seed): 0.476 RSpredict(seed): 0.230 Positive Predictive Value RNAalifold(seed): 0.844 RSpredict(seed): 0.598 Number of pairs reference - predicted secondary structure: 689 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.544 NanoFolder: 0.201 Sensitivity RNAalifold(seed): 0.340 NanoFolder: 0.231 Positive Predictive Value RNAalifold(seed): 0.873 NanoFolder: 0.178 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.550 Mastr(seed): 0.115 Sensitivity RNAalifold(seed): 0.359 Mastr(seed): 0.016 Positive Predictive Value RNAalifold(seed): 0.845 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 608 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidFold	51 TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.791 CentroidFold: 0.711 Sensitivity TurboFold(seed): 0.762 CentroidFold: 0.681 Positive Predictive Value TurboFold(seed): 0.822 CentroidFold: 0.743 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1223 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.742 CentroidFold: 0.570 Sensitivity PETfold_pre2.0(seed): 0.676 CentroidFold: 0.515 Positive Predictive Value PETfold_pre2.0(seed): 0.815 CentroidFold: 0.632 Number of pairs reference - predicted secondary structure: 1223 Wilcoxon single-rank test P-value: 3.56938820447e-08	1915 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.707 CentroidFold: 0.534 Sensitivity ContextFold: 0.670 CentroidFold: 0.475 Positive Predictive Value ContextFold: 0.746 CentroidFold: 0.600 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.787 CentroidFold: 0.650 Sensitivity TurboFold(20): 0.740 CentroidFold: 0.595 Positive Predictive Value TurboFold(20): 0.837 CentroidFold: 0.713 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	705 CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.751 CentroidFold: 0.598 Sensitivity CentroidAlifold(seed): 0.626 CentroidFold: 0.538 Positive Predictive Value CentroidAlifold(seed): 0.902 CentroidFold: 0.667 Number of pairs reference - predicted secondary structure: 705 Wilcoxon single-rank test P-value: 3.56938820447e-08	638 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.746 CentroidFold: 0.569 Sensitivity PETfold_pre2.0(20): 0.688 CentroidFold: 0.508 Positive Predictive Value PETfold_pre2.0(20): 0.809 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 638 Wilcoxon single-rank test P-value: 3.56938820447e-08	641 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.742 CentroidFold: 0.569 Sensitivity CentroidAlifold(20): 0.618 CentroidFold: 0.508 Positive Predictive Value CentroidAlifold(20): 0.892 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 CentroidFold: 0.602 Sensitivity CentroidHomfold‑LAST: 0.527 CentroidFold: 0.555 Positive Predictive Value CentroidHomfold‑LAST: 0.850 CentroidFold: 0.653 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.758 CentroidFold: 0.637 Sensitivity PPfold(20): 0.654 CentroidFold: 0.579 Positive Predictive Value PPfold(20): 0.879 CentroidFold: 0.702 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	641 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.689 CentroidFold: 0.569 Sensitivity RNAalifold(20): 0.602 CentroidFold: 0.508 Positive Predictive Value RNAalifold(20): 0.789 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	727 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.656 CentroidFold: 0.599 Sensitivity MXScarna(seed): 0.570 CentroidFold: 0.539 Positive Predictive Value MXScarna(seed): 0.756 CentroidFold: 0.667 Number of pairs reference - predicted secondary structure: 727 Wilcoxon single-rank test P-value: 3.56938820447e-08	641 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.649 CentroidFold: 0.569 Sensitivity MXScarna(20): 0.591 CentroidFold: 0.508 Positive Predictive Value MXScarna(20): 0.713 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	1915 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.565 CentroidFold: 0.534 Sensitivity IPknot: 0.504 CentroidFold: 0.475 Positive Predictive Value IPknot: 0.634 CentroidFold: 0.600 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.685 CentroidFold: 0.655 Sensitivity Multilign(20): 0.617 CentroidFold: 0.598 Positive Predictive Value Multilign(20): 0.762 CentroidFold: 0.718 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 Murlet(20) vs CentroidFold Matthews Correlation Coefficient Murlet(20): 0.629 CentroidFold: 0.627 Sensitivity Murlet(20): 0.503 CentroidFold: 0.569 Positive Predictive Value Murlet(20): 0.787 CentroidFold: 0.692 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 0.00610617588669	699 RNAalifold(seed) vs CentroidFold Matthews Correlation Coefficient RNAalifold(seed): 0.636 CentroidFold: 0.594 Sensitivity RNAalifold(seed): 0.483 CentroidFold: 0.533 Positive Predictive Value RNAalifold(seed): 0.837 CentroidFold: 0.662 Number of pairs reference - predicted secondary structure: 699 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.676 CentroidFold: 0.657 Sensitivity RNASampler(20): 0.522 CentroidFold: 0.616 Positive Predictive Value RNASampler(20): 0.877 CentroidFold: 0.703 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.534 Contrafold: 0.521 Sensitivity CentroidFold: 0.475 Contrafold: 0.506 Positive Predictive Value CentroidFold: 0.600 Contrafold: 0.537 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.534 Sfold: 0.488 Sensitivity CentroidFold: 0.475 Sfold: 0.440 Positive Predictive Value CentroidFold: 0.600 Sfold: 0.542 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs CentroidFold Matthews Correlation Coefficient Multilign(seed): 0.681 CentroidFold: 0.609 Sensitivity Multilign(seed): 0.649 CentroidFold: 0.588 Positive Predictive Value Multilign(seed): 0.717 CentroidFold: 0.633 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.534 MaxExpect: 0.480 Sensitivity CentroidFold: 0.475 MaxExpect: 0.469 Positive Predictive Value CentroidFold: 0.600 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.534 ProbKnot: 0.475 Sensitivity CentroidFold: 0.475 ProbKnot: 0.473 Positive Predictive Value CentroidFold: 0.600 ProbKnot: 0.479 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.534 Fold: 0.453 Sensitivity CentroidFold: 0.475 Fold: 0.458 Positive Predictive Value CentroidFold: 0.600 Fold: 0.449 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.646 RNASampler(seed): 0.629 Sensitivity CentroidFold: 0.570 RNASampler(seed): 0.468 Positive Predictive Value CentroidFold: 0.735 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.534 UNAFold: 0.454 Sensitivity CentroidFold: 0.475 UNAFold: 0.453 Positive Predictive Value CentroidFold: 0.600 UNAFold: 0.455 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.602 RNAsubopt: 0.525 Sensitivity CentroidFold: 0.555 RNAsubopt: 0.530 Positive Predictive Value CentroidFold: 0.653 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.569 RSpredict(20): 0.491 Sensitivity CentroidFold: 0.508 RSpredict(20): 0.405 Positive Predictive Value CentroidFold: 0.638 RSpredict(20): 0.595 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: 0.650 CMfinder(20): 0.549 Sensitivity CentroidFold: 0.594 CMfinder(20): 0.380 Positive Predictive Value CentroidFold: 0.712 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.553 PknotsRG: 0.466 Sensitivity CentroidFold: 0.494 PknotsRG: 0.467 Positive Predictive Value CentroidFold: 0.619 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.569 Carnac(20): 0.518 Sensitivity CentroidFold: 0.508 Carnac(20): 0.301 Positive Predictive Value CentroidFold: 0.638 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.534 RNAfold: 0.446 Sensitivity CentroidFold: 0.475 RNAfold: 0.449 Positive Predictive Value CentroidFold: 0.600 RNAfold: 0.443 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.671 CMfinder(seed): 0.486 Sensitivity CentroidFold: 0.617 CMfinder(seed): 0.312 Positive Predictive Value CentroidFold: 0.730 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.530 Afold: 0.441 Sensitivity CentroidFold: 0.468 Afold: 0.441 Positive Predictive Value CentroidFold: 0.601 Afold: 0.443 Number of pairs reference - predicted secondary structure: 1238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.645 HotKnots: 0.613 Sensitivity CentroidFold: 0.612 HotKnots: 0.607 Positive Predictive Value CentroidFold: 0.685 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.554 CRWrnafold: 0.437 Sensitivity CentroidFold: 0.497 CRWrnafold: 0.440 Positive Predictive Value CentroidFold: 0.619 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.656 Pknots: 0.606 Sensitivity CentroidFold: 0.620 Pknots: 0.595 Positive Predictive Value CentroidFold: 0.701 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.593 McQFold: 0.467 Sensitivity CentroidFold: 0.546 McQFold: 0.457 Positive Predictive Value CentroidFold: 0.646 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.601 RNAshapes: 0.477 Sensitivity CentroidFold: 0.554 RNAshapes: 0.472 Positive Predictive Value CentroidFold: 0.653 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.679 PPfold(seed): 0.626 Sensitivity CentroidFold: 0.654 PPfold(seed): 0.495 Positive Predictive Value CentroidFold: 0.707 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.578 Mastr(20): 0.298 Sensitivity CentroidFold: 0.523 Mastr(20): 0.112 Positive Predictive Value CentroidFold: 0.640 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.645 Murlet(seed): 0.540 Sensitivity CentroidFold: 0.594 Murlet(seed): 0.360 Positive Predictive Value CentroidFold: 0.701 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.601 RNASLOpt: 0.470 Sensitivity CentroidFold: 0.555 RNASLOpt: 0.442 Positive Predictive Value CentroidFold: 0.653 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.675 Cylofold: 0.575 Sensitivity CentroidFold: 0.640 Cylofold: 0.551 Positive Predictive Value CentroidFold: 0.717 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.570 RNAwolf: 0.343 Sensitivity CentroidFold: 0.515 RNAwolf: 0.358 Positive Predictive Value CentroidFold: 0.632 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.599 Vsfold4: 0.346 Sensitivity CentroidFold: 0.553 Vsfold4: 0.318 Positive Predictive Value CentroidFold: 0.651 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.600 Vsfold5: 0.339 Sensitivity CentroidFold: 0.553 Vsfold5: 0.322 Positive Predictive Value CentroidFold: 0.651 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.658 Alterna: 0.552 Sensitivity CentroidFold: 0.621 Alterna: 0.547 Positive Predictive Value CentroidFold: 0.703 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.658 RDfolder: 0.520 Sensitivity CentroidFold: 0.621 RDfolder: 0.464 Positive Predictive Value CentroidFold: 0.703 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.624 Carnac(seed): 0.244 Sensitivity CentroidFold: 0.589 Carnac(seed): 0.069 Positive Predictive Value CentroidFold: 0.662 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.655 MCFold: 0.473 Sensitivity CentroidFold: 0.618 MCFold: 0.524 Positive Predictive Value CentroidFold: 0.699 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.600 RSpredict(seed): 0.373 Sensitivity CentroidFold: 0.540 RSpredict(seed): 0.231 Positive Predictive Value CentroidFold: 0.667 RSpredict(seed): 0.605 Number of pairs reference - predicted secondary structure: 701 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.619 NanoFolder: 0.194 Sensitivity CentroidFold: 0.569 NanoFolder: 0.229 Positive Predictive Value CentroidFold: 0.676 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.637 Mastr(seed): 0.114 Sensitivity CentroidFold: 0.587 Mastr(seed): 0.016 Positive Predictive Value CentroidFold: 0.692 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(20)	19 TurboFold(seed) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 RNASampler(20): 0.571 Sensitivity TurboFold(seed): 0.851 RNASampler(20): 0.345 Positive Predictive Value TurboFold(seed): 0.867 RNASampler(20): 0.950 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.08252958266e-08	380 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.830 RNASampler(20): 0.694 Sensitivity PETfold_pre2.0(seed): 0.766 RNASampler(20): 0.551 Positive Predictive Value PETfold_pre2.0(seed): 0.901 RNASampler(20): 0.876 Number of pairs reference - predicted secondary structure: 380 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.860 RNASampler(20): 0.676 Sensitivity ContextFold: 0.827 RNASampler(20): 0.522 Positive Predictive Value ContextFold: 0.895 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.816 RNASampler(20): 0.676 Sensitivity TurboFold(20): 0.780 RNASampler(20): 0.522 Positive Predictive Value TurboFold(20): 0.856 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	178 CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.792 RNASampler(20): 0.590 Sensitivity CentroidAlifold(seed): 0.674 RNASampler(20): 0.389 Positive Predictive Value CentroidAlifold(seed): 0.931 RNASampler(20): 0.898 Number of pairs reference - predicted secondary structure: 178 Wilcoxon single-rank test P-value: 3.56938820447e-08	391 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.779 RNASampler(20): 0.677 Sensitivity PETfold_pre2.0(20): 0.680 RNASampler(20): 0.524 Positive Predictive Value PETfold_pre2.0(20): 0.894 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 391 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.790 RNASampler(20): 0.676 Sensitivity CentroidAlifold(20): 0.677 RNASampler(20): 0.522 Positive Predictive Value CentroidAlifold(20): 0.923 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.794 RNASampler(20): 0.676 Sensitivity CentroidHomfold‑LAST: 0.706 RNASampler(20): 0.522 Positive Predictive Value CentroidHomfold‑LAST: 0.894 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	388 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.769 RNASampler(20): 0.677 Sensitivity PPfold(20): 0.648 RNASampler(20): 0.524 Positive Predictive Value PPfold(20): 0.912 RNASampler(20): 0.876 Number of pairs reference - predicted secondary structure: 388 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.744 RNASampler(20): 0.676 Sensitivity RNAalifold(20): 0.623 RNASampler(20): 0.522 Positive Predictive Value RNAalifold(20): 0.889 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	190 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.788 RNASampler(20): 0.605 Sensitivity MXScarna(seed): 0.740 RNASampler(20): 0.405 Positive Predictive Value MXScarna(seed): 0.840 RNASampler(20): 0.904 Number of pairs reference - predicted secondary structure: 190 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 MXScarna(20) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(20): 0.748 RNASampler(20): 0.676 Sensitivity MXScarna(20): 0.705 RNASampler(20): 0.522 Positive Predictive Value MXScarna(20): 0.794 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.713 RNASampler(20): 0.676 Sensitivity IPknot: 0.674 RNASampler(20): 0.522 Positive Predictive Value IPknot: 0.756 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	372 Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.712 RNASampler(20): 0.685 Sensitivity Multilign(20): 0.639 RNASampler(20): 0.533 Positive Predictive Value Multilign(20): 0.795 RNASampler(20): 0.881 Number of pairs reference - predicted secondary structure: 372 Wilcoxon single-rank test P-value: 3.56938820447e-08	383 Murlet(20) vs RNASampler(20) Matthews Correlation Coefficient Murlet(20): 0.694 RNASampler(20): 0.689 Sensitivity Murlet(20): 0.574 RNASampler(20): 0.541 Positive Predictive Value Murlet(20): 0.841 RNASampler(20): 0.878 Number of pairs reference - predicted secondary structure: 383 Wilcoxon single-rank test P-value: 4.48494289621e-08	174 RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.624 RNASampler(20): 0.584 Sensitivity RNAalifold(seed): 0.413 RNASampler(20): 0.381 Positive Predictive Value RNAalifold(seed): 0.944 RNASampler(20): 0.896 Number of pairs reference - predicted secondary structure: 174 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.676 CentroidFold: 0.657 Sensitivity RNASampler(20): 0.522 CentroidFold: 0.616 Positive Predictive Value RNASampler(20): 0.877 CentroidFold: 0.703 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.676 Contrafold: 0.645 Sensitivity RNASampler(20): 0.522 Contrafold: 0.637 Positive Predictive Value RNASampler(20): 0.877 Contrafold: 0.656 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.676 Sfold: 0.617 Sensitivity RNASampler(20): 0.522 Sfold: 0.571 Positive Predictive Value RNASampler(20): 0.877 Sfold: 0.669 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.536 Multilign(seed): 0.334 Sensitivity RNASampler(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value RNASampler(20): 0.833 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.676 MaxExpect: 0.624 Sensitivity RNASampler(20): 0.522 MaxExpect: 0.614 Positive Predictive Value RNASampler(20): 0.877 MaxExpect: 0.636 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.676 ProbKnot: 0.620 Sensitivity RNASampler(20): 0.522 ProbKnot: 0.617 Positive Predictive Value RNASampler(20): 0.877 ProbKnot: 0.624 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.676 Fold: 0.622 Sensitivity RNASampler(20): 0.522 Fold: 0.623 Positive Predictive Value RNASampler(20): 0.877 Fold: 0.623 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): 0.640 RNASampler(seed): 0.571 Sensitivity RNASampler(20): 0.454 RNASampler(seed): 0.343 Positive Predictive Value RNASampler(20): 0.909 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.676 UNAFold: 0.598 Sensitivity RNASampler(20): 0.522 UNAFold: 0.591 Positive Predictive Value RNASampler(20): 0.877 UNAFold: 0.606 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.676 RNAsubopt: 0.583 Sensitivity RNASampler(20): 0.522 RNAsubopt: 0.587 Positive Predictive Value RNASampler(20): 0.877 RNAsubopt: 0.580 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RSpredict(20) vs RNASampler(20) Matthews Correlation Coefficient RSpredict(20): 0.695 RNASampler(20): 0.676 Sensitivity RSpredict(20): 0.612 RNASampler(20): 0.522 Positive Predictive Value RSpredict(20): 0.790 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.677 CMfinder(20): 0.596 Sensitivity RNASampler(20): 0.524 CMfinder(20): 0.436 Positive Predictive Value RNASampler(20): 0.877 CMfinder(20): 0.815 Number of pairs reference - predicted secondary structure: 389 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.676 PknotsRG: 0.588 Sensitivity RNASampler(20): 0.522 PknotsRG: 0.589 Positive Predictive Value RNASampler(20): 0.877 PknotsRG: 0.589 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.676 Carnac(20): 0.586 Sensitivity RNASampler(20): 0.522 Carnac(20): 0.385 Positive Predictive Value RNASampler(20): 0.877 Carnac(20): 0.894 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.676 RNAfold: 0.594 Sensitivity RNASampler(20): 0.522 RNAfold: 0.595 Positive Predictive Value RNASampler(20): 0.877 RNAfold: 0.596 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs RNASampler(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RNASampler(20): 0.593 Sensitivity CMfinder(seed): 0.607 RNASampler(20): 0.399 Positive Predictive Value CMfinder(seed): 0.898 RNASampler(20): 0.888 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.620 Afold: 0.613 Sensitivity RNASampler(20): 0.433 Afold: 0.606 Positive Predictive Value RNASampler(20): 0.889 Afold: 0.622 Number of pairs reference - predicted secondary structure: 195 Wilcoxon single-rank test P-value: 3.09925167801e-06	+ RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.770 HotKnots: 0.698 Sensitivity RNASampler(20): 0.622 HotKnots: 0.694 Positive Predictive Value RNASampler(20): 0.957 HotKnots: 0.706 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.676 CRWrnafold: 0.609 Sensitivity RNASampler(20): 0.522 CRWrnafold: 0.605 Positive Predictive Value RNASampler(20): 0.877 CRWrnafold: 0.614 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.857 Pknots: 0.660 Sensitivity RNASampler(20): 0.758 Pknots: 0.666 Positive Predictive Value RNASampler(20): 0.971 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.676 McQFold: 0.504 Sensitivity RNASampler(20): 0.522 McQFold: 0.487 Positive Predictive Value RNASampler(20): 0.877 McQFold: 0.525 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.677 RNAshapes: 0.560 Sensitivity RNASampler(20): 0.522 RNAshapes: 0.556 Positive Predictive Value RNASampler(20): 0.879 RNAshapes: 0.566 Number of pairs reference - predicted secondary structure: 392 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.620 PPfold(seed): 0.453 Sensitivity RNASampler(20): 0.407 PPfold(seed): 0.224 Positive Predictive Value RNASampler(20): 0.949 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.676 Mastr(20): 0.510 Sensitivity RNASampler(20): 0.522 Mastr(20): 0.331 Positive Predictive Value RNASampler(20): 0.877 Mastr(20): 0.789 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.643 Murlet(seed): 0.631 Sensitivity RNASampler(20): 0.454 Murlet(seed): 0.418 Positive Predictive Value RNASampler(20): 0.913 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 0.000579628272742	+ RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.676 RNASLOpt: 0.520 Sensitivity RNASampler(20): 0.522 RNASLOpt: 0.488 Positive Predictive Value RNASampler(20): 0.877 RNASLOpt: 0.557 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.773 Cylofold: 0.559 Sensitivity RNASampler(20): 0.625 Cylofold: 0.546 Positive Predictive Value RNASampler(20): 0.959 Cylofold: 0.579 Number of pairs reference - predicted secondary structure: 299 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.676 RNAwolf: 0.445 Sensitivity RNASampler(20): 0.522 RNAwolf: 0.457 Positive Predictive Value RNASampler(20): 0.877 RNAwolf: 0.437 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.676 Vsfold4: 0.356 Sensitivity RNASampler(20): 0.522 Vsfold4: 0.330 Positive Predictive Value RNASampler(20): 0.877 Vsfold4: 0.388 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.676 Vsfold5: 0.331 Sensitivity RNASampler(20): 0.522 Vsfold5: 0.315 Positive Predictive Value RNASampler(20): 0.877 Vsfold5: 0.352 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.859 Alterna: 0.620 Sensitivity RNASampler(20): 0.761 Alterna: 0.627 Positive Predictive Value RNASampler(20): 0.971 Alterna: 0.618 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.859 RDfolder: 0.560 Sensitivity RNASampler(20): 0.761 RDfolder: 0.516 Positive Predictive Value RNASampler(20): 0.971 RDfolder: 0.614 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.591 Carnac(seed): 0.338 Sensitivity RNASampler(20): 0.381 Carnac(seed): 0.127 Positive Predictive Value RNASampler(20): 0.920 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.771 MCFold: 0.500 Sensitivity RNASampler(20): 0.623 MCFold: 0.560 Positive Predictive Value RNASampler(20): 0.956 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.590 RSpredict(seed): 0.444 Sensitivity RNASampler(20): 0.389 RSpredict(seed): 0.303 Positive Predictive Value RNASampler(20): 0.898 RSpredict(seed): 0.653 Number of pairs reference - predicted secondary structure: 178 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.672 NanoFolder: 0.235 Sensitivity RNASampler(20): 0.506 NanoFolder: 0.278 Positive Predictive Value RNASampler(20): 0.893 NanoFolder: 0.202 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.606 Mastr(seed): 0.187 Sensitivity RNASampler(20): 0.406 Mastr(seed): 0.043 Positive Predictive Value RNASampler(20): 0.905 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08
Contrafold	51 TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.791 Contrafold: 0.704 Sensitivity TurboFold(seed): 0.762 Contrafold: 0.703 Positive Predictive Value TurboFold(seed): 0.822 Contrafold: 0.706 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1224 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 Contrafold: 0.554 Sensitivity PETfold_pre2.0(seed): 0.675 Contrafold: 0.540 Positive Predictive Value PETfold_pre2.0(seed): 0.814 Contrafold: 0.569 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.686 Contrafold: 0.521 Sensitivity ContextFold: 0.648 Contrafold: 0.506 Positive Predictive Value ContextFold: 0.725 Contrafold: 0.537 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.787 Contrafold: 0.638 Sensitivity TurboFold(20): 0.740 Contrafold: 0.620 Positive Predictive Value TurboFold(20): 0.837 Contrafold: 0.658 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 Contrafold: 0.584 Sensitivity CentroidAlifold(seed): 0.623 Contrafold: 0.565 Positive Predictive Value CentroidAlifold(seed): 0.901 Contrafold: 0.604 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 Contrafold: 0.553 Sensitivity PETfold_pre2.0(20): 0.686 Contrafold: 0.536 Positive Predictive Value PETfold_pre2.0(20): 0.807 Contrafold: 0.572 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 Contrafold: 0.554 Sensitivity CentroidAlifold(20): 0.616 Contrafold: 0.536 Positive Predictive Value CentroidAlifold(20): 0.891 Contrafold: 0.572 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 Contrafold: 0.588 Sensitivity CentroidHomfold‑LAST: 0.527 Contrafold: 0.578 Positive Predictive Value CentroidHomfold‑LAST: 0.850 Contrafold: 0.600 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.758 Contrafold: 0.624 Sensitivity PPfold(20): 0.654 Contrafold: 0.605 Positive Predictive Value PPfold(20): 0.879 Contrafold: 0.644 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.687 Contrafold: 0.554 Sensitivity RNAalifold(20): 0.600 Contrafold: 0.536 Positive Predictive Value RNAalifold(20): 0.787 Contrafold: 0.572 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	728 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.654 Contrafold: 0.585 Sensitivity MXScarna(seed): 0.568 Contrafold: 0.566 Positive Predictive Value MXScarna(seed): 0.753 Contrafold: 0.605 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.647 Contrafold: 0.554 Sensitivity MXScarna(20): 0.589 Contrafold: 0.536 Positive Predictive Value MXScarna(20): 0.710 Contrafold: 0.572 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1972 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.563 Contrafold: 0.522 Sensitivity IPknot: 0.501 Contrafold: 0.507 Positive Predictive Value IPknot: 0.632 Contrafold: 0.539 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.685 Contrafold: 0.642 Sensitivity Multilign(20): 0.617 Contrafold: 0.624 Positive Predictive Value Multilign(20): 0.762 Contrafold: 0.662 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.629 Contrafold: 0.613 Sensitivity Murlet(20): 0.503 Contrafold: 0.595 Positive Predictive Value Murlet(20): 0.787 Contrafold: 0.632 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.85233844192e-08	700 RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.634 Contrafold: 0.579 Sensitivity RNAalifold(seed): 0.482 Contrafold: 0.560 Positive Predictive Value RNAalifold(seed): 0.835 Contrafold: 0.598 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	1915 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.534 Contrafold: 0.521 Sensitivity CentroidFold: 0.475 Contrafold: 0.506 Positive Predictive Value CentroidFold: 0.600 Contrafold: 0.537 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.676 Contrafold: 0.645 Sensitivity RNASampler(20): 0.522 Contrafold: 0.637 Positive Predictive Value RNASampler(20): 0.877 Contrafold: 0.656 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.521 Sfold: 0.481 Sensitivity Contrafold: 0.506 Sfold: 0.433 Positive Predictive Value Contrafold: 0.537 Sfold: 0.535 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs Contrafold Matthews Correlation Coefficient Multilign(seed): 0.681 Contrafold: 0.598 Sensitivity Multilign(seed): 0.649 Contrafold: 0.599 Positive Predictive Value Multilign(seed): 0.717 Contrafold: 0.598 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.521 MaxExpect: 0.476 Sensitivity Contrafold: 0.506 MaxExpect: 0.465 Positive Predictive Value Contrafold: 0.537 MaxExpect: 0.488 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.521 ProbKnot: 0.471 Sensitivity Contrafold: 0.506 ProbKnot: 0.468 Positive Predictive Value Contrafold: 0.537 ProbKnot: 0.475 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.521 Fold: 0.448 Sensitivity Contrafold: 0.506 Fold: 0.453 Positive Predictive Value Contrafold: 0.537 Fold: 0.444 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.639 RNASampler(seed): 0.629 Sensitivity Contrafold: 0.603 RNASampler(seed): 0.468 Positive Predictive Value Contrafold: 0.679 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 2.82781450476e-07	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.521 UNAFold: 0.447 Sensitivity Contrafold: 0.506 UNAFold: 0.446 Positive Predictive Value Contrafold: 0.537 UNAFold: 0.448 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.588 RNAsubopt: 0.525 Sensitivity Contrafold: 0.578 RNAsubopt: 0.530 Positive Predictive Value Contrafold: 0.600 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.554 RSpredict(20): 0.487 Sensitivity Contrafold: 0.536 RSpredict(20): 0.402 Positive Predictive Value Contrafold: 0.572 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.638 CMfinder(20): 0.549 Sensitivity Contrafold: 0.619 CMfinder(20): 0.380 Positive Predictive Value Contrafold: 0.658 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.541 PknotsRG: 0.466 Sensitivity Contrafold: 0.524 PknotsRG: 0.467 Positive Predictive Value Contrafold: 0.558 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.554 Carnac(20): 0.518 Sensitivity Contrafold: 0.536 Carnac(20): 0.301 Positive Predictive Value Contrafold: 0.572 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.521 RNAfold: 0.440 Sensitivity Contrafold: 0.506 RNAfold: 0.443 Positive Predictive Value Contrafold: 0.537 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.658 CMfinder(seed): 0.486 Sensitivity Contrafold: 0.642 CMfinder(seed): 0.312 Positive Predictive Value Contrafold: 0.676 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.516 Afold: 0.434 Sensitivity Contrafold: 0.497 Afold: 0.433 Positive Predictive Value Contrafold: 0.535 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.644 HotKnots: 0.613 Sensitivity Contrafold: 0.635 HotKnots: 0.607 Positive Predictive Value Contrafold: 0.658 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.542 CRWrnafold: 0.437 Sensitivity Contrafold: 0.526 CRWrnafold: 0.440 Positive Predictive Value Contrafold: 0.559 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.656 Pknots: 0.606 Sensitivity Contrafold: 0.645 Pknots: 0.595 Positive Predictive Value Contrafold: 0.673 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.580 McQFold: 0.467 Sensitivity Contrafold: 0.570 McQFold: 0.457 Positive Predictive Value Contrafold: 0.592 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.588 RNAshapes: 0.477 Sensitivity Contrafold: 0.577 RNAshapes: 0.472 Positive Predictive Value Contrafold: 0.600 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.676 PPfold(seed): 0.626 Sensitivity Contrafold: 0.676 PPfold(seed): 0.495 Positive Predictive Value Contrafold: 0.677 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.561 Mastr(20): 0.296 Sensitivity Contrafold: 0.547 Mastr(20): 0.111 Positive Predictive Value Contrafold: 0.577 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.637 Murlet(seed): 0.540 Sensitivity Contrafold: 0.619 Murlet(seed): 0.360 Positive Predictive Value Contrafold: 0.657 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.589 RNASLOpt: 0.470 Sensitivity Contrafold: 0.579 RNASLOpt: 0.442 Positive Predictive Value Contrafold: 0.601 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.673 Cylofold: 0.575 Sensitivity Contrafold: 0.662 Cylofold: 0.551 Positive Predictive Value Contrafold: 0.689 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.558 RNAwolf: 0.343 Sensitivity Contrafold: 0.544 RNAwolf: 0.358 Positive Predictive Value Contrafold: 0.574 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.586 Vsfold4: 0.346 Sensitivity Contrafold: 0.576 Vsfold4: 0.318 Positive Predictive Value Contrafold: 0.598 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.587 Vsfold5: 0.339 Sensitivity Contrafold: 0.577 Vsfold5: 0.322 Positive Predictive Value Contrafold: 0.599 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.657 Alterna: 0.552 Sensitivity Contrafold: 0.646 Alterna: 0.547 Positive Predictive Value Contrafold: 0.675 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.657 RDfolder: 0.520 Sensitivity Contrafold: 0.646 RDfolder: 0.464 Positive Predictive Value Contrafold: 0.675 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.614 Carnac(seed): 0.244 Sensitivity Contrafold: 0.610 Carnac(seed): 0.069 Positive Predictive Value Contrafold: 0.618 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.654 MCFold: 0.473 Sensitivity Contrafold: 0.642 MCFold: 0.524 Positive Predictive Value Contrafold: 0.672 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.585 RSpredict(seed): 0.369 Sensitivity Contrafold: 0.567 RSpredict(seed): 0.229 Positive Predictive Value Contrafold: 0.605 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.603 NanoFolder: 0.194 Sensitivity Contrafold: 0.591 NanoFolder: 0.229 Positive Predictive Value Contrafold: 0.618 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.622 Mastr(seed): 0.113 Sensitivity Contrafold: 0.608 Mastr(seed): 0.016 Positive Predictive Value Contrafold: 0.637 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08
Sfold	51 TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.791 Sfold: 0.690 Sensitivity TurboFold(seed): 0.762 Sfold: 0.665 Positive Predictive Value TurboFold(seed): 0.822 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1224 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 Sfold: 0.525 Sensitivity PETfold_pre2.0(seed): 0.675 Sfold: 0.475 Positive Predictive Value PETfold_pre2.0(seed): 0.814 Sfold: 0.580 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.686 Sfold: 0.481 Sensitivity ContextFold: 0.648 Sfold: 0.433 Positive Predictive Value ContextFold: 0.725 Sfold: 0.535 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.787 Sfold: 0.613 Sensitivity TurboFold(20): 0.740 Sfold: 0.556 Positive Predictive Value TurboFold(20): 0.837 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 Sfold: 0.570 Sensitivity CentroidAlifold(seed): 0.623 Sfold: 0.514 Positive Predictive Value CentroidAlifold(seed): 0.901 Sfold: 0.632 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 Sfold: 0.529 Sensitivity PETfold_pre2.0(20): 0.686 Sfold: 0.475 Positive Predictive Value PETfold_pre2.0(20): 0.807 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 Sfold: 0.530 Sensitivity CentroidAlifold(20): 0.616 Sfold: 0.475 Positive Predictive Value CentroidAlifold(20): 0.891 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 Sfold: 0.562 Sensitivity CentroidHomfold‑LAST: 0.527 Sfold: 0.516 Positive Predictive Value CentroidHomfold‑LAST: 0.850 Sfold: 0.614 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.758 Sfold: 0.603 Sensitivity PPfold(20): 0.654 Sfold: 0.542 Positive Predictive Value PPfold(20): 0.879 Sfold: 0.671 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.687 Sfold: 0.530 Sensitivity RNAalifold(20): 0.600 Sfold: 0.475 Positive Predictive Value RNAalifold(20): 0.787 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	728 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.654 Sfold: 0.571 Sensitivity MXScarna(seed): 0.568 Sfold: 0.515 Positive Predictive Value MXScarna(seed): 0.753 Sfold: 0.633 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.647 Sfold: 0.530 Sensitivity MXScarna(20): 0.589 Sfold: 0.475 Positive Predictive Value MXScarna(20): 0.710 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1972 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.563 Sfold: 0.482 Sensitivity IPknot: 0.501 Sfold: 0.433 Positive Predictive Value IPknot: 0.632 Sfold: 0.536 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.685 Sfold: 0.614 Sensitivity Multilign(20): 0.617 Sfold: 0.557 Positive Predictive Value Multilign(20): 0.762 Sfold: 0.678 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.629 Sfold: 0.591 Sensitivity Murlet(20): 0.503 Sfold: 0.532 Positive Predictive Value Murlet(20): 0.787 Sfold: 0.657 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	700 RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.634 Sfold: 0.565 Sensitivity RNAalifold(seed): 0.482 Sfold: 0.509 Positive Predictive Value RNAalifold(seed): 0.835 Sfold: 0.627 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	1915 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.534 Sfold: 0.488 Sensitivity CentroidFold: 0.475 Sfold: 0.440 Positive Predictive Value CentroidFold: 0.600 Sfold: 0.542 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.676 Sfold: 0.617 Sensitivity RNASampler(20): 0.522 Sfold: 0.571 Positive Predictive Value RNASampler(20): 0.877 Sfold: 0.669 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.521 Sfold: 0.481 Sensitivity Contrafold: 0.506 Sfold: 0.433 Positive Predictive Value Contrafold: 0.537 Sfold: 0.535 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.681 Sfold: 0.577 Sensitivity Multilign(seed): 0.649 Sfold: 0.557 Positive Predictive Value Multilign(seed): 0.717 Sfold: 0.599 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Sfold vs MaxExpect Matthews Correlation Coefficient Sfold: 0.481 MaxExpect: 0.476 Sensitivity Sfold: 0.433 MaxExpect: 0.465 Positive Predictive Value Sfold: 0.535 MaxExpect: 0.488 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.481 ProbKnot: 0.471 Sensitivity Sfold: 0.433 ProbKnot: 0.468 Positive Predictive Value Sfold: 0.535 ProbKnot: 0.475 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.481 Fold: 0.448 Sensitivity Sfold: 0.433 Fold: 0.453 Positive Predictive Value Sfold: 0.535 Fold: 0.444 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs Sfold Matthews Correlation Coefficient RNASampler(seed): 0.629 Sfold: 0.603 Sensitivity RNASampler(seed): 0.468 Sfold: 0.554 Positive Predictive Value RNASampler(seed): 0.847 Sfold: 0.659 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.481 UNAFold: 0.447 Sensitivity Sfold: 0.433 UNAFold: 0.446 Positive Predictive Value Sfold: 0.535 UNAFold: 0.448 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.562 RNAsubopt: 0.525 Sensitivity Sfold: 0.516 RNAsubopt: 0.530 Positive Predictive Value Sfold: 0.614 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.530 RSpredict(20): 0.487 Sensitivity Sfold: 0.475 RSpredict(20): 0.402 Positive Predictive Value Sfold: 0.591 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.613 CMfinder(20): 0.549 Sensitivity Sfold: 0.556 CMfinder(20): 0.380 Positive Predictive Value Sfold: 0.677 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.508 PknotsRG: 0.466 Sensitivity Sfold: 0.459 PknotsRG: 0.467 Positive Predictive Value Sfold: 0.563 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.530 Carnac(20): 0.518 Sensitivity Sfold: 0.475 Carnac(20): 0.301 Positive Predictive Value Sfold: 0.591 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.481 RNAfold: 0.440 Sensitivity Sfold: 0.433 RNAfold: 0.443 Positive Predictive Value Sfold: 0.535 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CMfinder(seed) Matthews Correlation Coefficient Sfold: 0.645 CMfinder(seed): 0.486 Sensitivity Sfold: 0.594 CMfinder(seed): 0.312 Positive Predictive Value Sfold: 0.703 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.482 Afold: 0.434 Sensitivity Sfold: 0.431 Afold: 0.433 Positive Predictive Value Sfold: 0.539 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.617 HotKnots: 0.613 Sensitivity Sfold: 0.581 HotKnots: 0.607 Positive Predictive Value Sfold: 0.662 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.510 CRWrnafold: 0.437 Sensitivity Sfold: 0.461 CRWrnafold: 0.440 Positive Predictive Value Sfold: 0.565 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs Sfold Matthews Correlation Coefficient Pknots: 0.606 Sfold: 0.601 Sensitivity Pknots: 0.595 Sfold: 0.565 Positive Predictive Value Pknots: 0.624 Sfold: 0.648 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 5.19883461079e-06	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.552 McQFold: 0.467 Sensitivity Sfold: 0.507 McQFold: 0.457 Positive Predictive Value Sfold: 0.602 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.562 RNAshapes: 0.477 Sensitivity Sfold: 0.516 RNAshapes: 0.472 Positive Predictive Value Sfold: 0.615 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.682 PPfold(seed): 0.626 Sensitivity Sfold: 0.657 PPfold(seed): 0.495 Positive Predictive Value Sfold: 0.709 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.534 Mastr(20): 0.296 Sensitivity Sfold: 0.482 Mastr(20): 0.111 Positive Predictive Value Sfold: 0.593 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.613 Murlet(seed): 0.540 Sensitivity Sfold: 0.572 Murlet(seed): 0.360 Positive Predictive Value Sfold: 0.658 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.564 RNASLOpt: 0.470 Sensitivity Sfold: 0.518 RNASLOpt: 0.442 Positive Predictive Value Sfold: 0.615 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.642 Cylofold: 0.575 Sensitivity Sfold: 0.603 Cylofold: 0.551 Positive Predictive Value Sfold: 0.688 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.525 RNAwolf: 0.343 Sensitivity Sfold: 0.477 RNAwolf: 0.358 Positive Predictive Value Sfold: 0.579 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.561 Vsfold4: 0.346 Sensitivity Sfold: 0.515 Vsfold4: 0.318 Positive Predictive Value Sfold: 0.613 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.561 Vsfold5: 0.339 Sensitivity Sfold: 0.515 Vsfold5: 0.322 Positive Predictive Value Sfold: 0.613 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.603 Alterna: 0.552 Sensitivity Sfold: 0.566 Alterna: 0.547 Positive Predictive Value Sfold: 0.649 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.603 RDfolder: 0.520 Sensitivity Sfold: 0.566 RDfolder: 0.464 Positive Predictive Value Sfold: 0.649 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.624 Carnac(seed): 0.244 Sensitivity Sfold: 0.583 Carnac(seed): 0.069 Positive Predictive Value Sfold: 0.668 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.621 MCFold: 0.473 Sensitivity Sfold: 0.583 MCFold: 0.524 Positive Predictive Value Sfold: 0.668 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.571 RSpredict(seed): 0.369 Sensitivity Sfold: 0.516 RSpredict(seed): 0.229 Positive Predictive Value Sfold: 0.633 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.583 NanoFolder: 0.194 Sensitivity Sfold: 0.531 NanoFolder: 0.229 Positive Predictive Value Sfold: 0.641 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.613 Mastr(seed): 0.113 Sensitivity Sfold: 0.563 Mastr(seed): 0.016 Positive Predictive Value Sfold: 0.670 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08
Multilign(seed)	22 TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.740 Multilign(seed): 0.698 Sensitivity TurboFold(seed): 0.698 Multilign(seed): 0.660 Positive Predictive Value TurboFold(seed): 0.784 Multilign(seed): 0.741 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	22 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.757 Multilign(seed): 0.698 Sensitivity PETfold_pre2.0(seed): 0.709 Multilign(seed): 0.660 Positive Predictive Value PETfold_pre2.0(seed): 0.809 Multilign(seed): 0.741 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 Multilign(seed) vs ContextFold Matthews Correlation Coefficient Multilign(seed): 0.681 ContextFold: 0.612 Sensitivity Multilign(seed): 0.649 ContextFold: 0.592 Positive Predictive Value Multilign(seed): 0.717 ContextFold: 0.633 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	3 TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): 0.571 Multilign(seed): 0.334 Sensitivity TurboFold(20): 0.512 Multilign(seed): 0.186 Positive Predictive Value TurboFold(20): 0.647 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	22 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.777 Multilign(seed): 0.698 Sensitivity CentroidAlifold(seed): 0.703 Multilign(seed): 0.660 Positive Predictive Value CentroidAlifold(seed): 0.859 Multilign(seed): 0.741 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	3 PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.473 Multilign(seed): 0.334 Sensitivity PETfold_pre2.0(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value PETfold_pre2.0(20): 0.700 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.693 Multilign(seed): 0.334 Sensitivity CentroidAlifold(20): 0.581 Multilign(seed): 0.186 Positive Predictive Value CentroidAlifold(20): 0.833 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	23 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.684 Multilign(seed): 0.681 Sensitivity CentroidHomfold‑LAST: 0.581 Multilign(seed): 0.649 Positive Predictive Value CentroidHomfold‑LAST: 0.806 Multilign(seed): 0.717 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.00027446829016	3 PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.531 Multilign(seed): 0.334 Sensitivity PPfold(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value PPfold(20): 0.875 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): 0.568 Multilign(seed): 0.334 Sensitivity RNAalifold(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value RNAalifold(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	22 Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.698 MXScarna(seed): 0.686 Sensitivity Multilign(seed): 0.660 MXScarna(seed): 0.662 Positive Predictive Value Multilign(seed): 0.741 MXScarna(seed): 0.712 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 1.27663599501e-06	3 MXScarna(20) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(20): 0.749 Multilign(seed): 0.334 Sensitivity MXScarna(20): 0.698 Multilign(seed): 0.186 Positive Predictive Value MXScarna(20): 0.811 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	23 Multilign(seed) vs IPknot Matthews Correlation Coefficient Multilign(seed): 0.681 IPknot: 0.642 Sensitivity Multilign(seed): 0.649 IPknot: 0.625 Positive Predictive Value Multilign(seed): 0.717 IPknot: 0.661 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.59469103578e-08	3 Multilign(20) vs Multilign(seed) Matthews Correlation Coefficient Multilign(20): 0.588 Multilign(seed): 0.334 Sensitivity Multilign(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value Multilign(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): 0.568 Multilign(seed): 0.334 Sensitivity Murlet(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value Murlet(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	22 RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.747 Multilign(seed): 0.698 Sensitivity RNAalifold(seed): 0.633 Multilign(seed): 0.660 Positive Predictive Value RNAalifold(seed): 0.883 Multilign(seed): 0.741 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	23 Multilign(seed) vs CentroidFold Matthews Correlation Coefficient Multilign(seed): 0.681 CentroidFold: 0.609 Sensitivity Multilign(seed): 0.649 CentroidFold: 0.588 Positive Predictive Value Multilign(seed): 0.717 CentroidFold: 0.633 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	3 RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.536 Multilign(seed): 0.334 Sensitivity RNASampler(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value RNASampler(20): 0.833 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	23 Multilign(seed) vs Contrafold Matthews Correlation Coefficient Multilign(seed): 0.681 Contrafold: 0.598 Sensitivity Multilign(seed): 0.649 Contrafold: 0.599 Positive Predictive Value Multilign(seed): 0.717 Contrafold: 0.598 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	23 Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.681 Sfold: 0.577 Sensitivity Multilign(seed): 0.649 Sfold: 0.557 Positive Predictive Value Multilign(seed): 0.717 Sfold: 0.599 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08		+ Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.681 MaxExpect: 0.554 Sensitivity Multilign(seed): 0.649 MaxExpect: 0.562 Positive Predictive Value Multilign(seed): 0.717 MaxExpect: 0.548 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.681 ProbKnot: 0.566 Sensitivity Multilign(seed): 0.649 ProbKnot: 0.578 Positive Predictive Value Multilign(seed): 0.717 ProbKnot: 0.556 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.681 Fold: 0.550 Sensitivity Multilign(seed): 0.649 Fold: 0.561 Positive Predictive Value Multilign(seed): 0.717 Fold: 0.541 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.753 RNASampler(seed): 0.702 Sensitivity Multilign(seed): 0.684 RNASampler(seed): 0.572 Positive Predictive Value Multilign(seed): 0.830 RNASampler(seed): 0.864 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.7968284078e-08	+ Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.681 UNAFold: 0.543 Sensitivity Multilign(seed): 0.649 UNAFold: 0.552 Positive Predictive Value Multilign(seed): 0.717 UNAFold: 0.537 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.681 RNAsubopt: 0.557 Sensitivity Multilign(seed): 0.649 RNAsubopt: 0.569 Positive Predictive Value Multilign(seed): 0.717 RNAsubopt: 0.548 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	? RSpredict(20) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(20): 0.739 Multilign(seed): 0.334 Sensitivity RSpredict(20): 0.698 Multilign(seed): 0.186 Positive Predictive Value RSpredict(20): 0.789 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Multilign(seed) Matthews Correlation Coefficient CMfinder(20): 0.514 Multilign(seed): 0.334 Sensitivity CMfinder(20): 0.395 Multilign(seed): 0.186 Positive Predictive Value CMfinder(20): 0.680 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Multilign(seed) vs PknotsRG Matthews Correlation Coefficient Multilign(seed): 0.681 PknotsRG: 0.600 Sensitivity Multilign(seed): 0.649 PknotsRG: 0.615 Positive Predictive Value Multilign(seed): 0.717 PknotsRG: 0.586 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Carnac(20) vs Multilign(seed) Matthews Correlation Coefficient Carnac(20): 0.588 Multilign(seed): 0.334 Sensitivity Carnac(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value Carnac(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.681 RNAfold: 0.593 Sensitivity Multilign(seed): 0.649 RNAfold: 0.604 Positive Predictive Value Multilign(seed): 0.717 RNAfold: 0.585 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): 0.767 CMfinder(seed): 0.531 Sensitivity Multilign(seed): 0.697 CMfinder(seed): 0.393 Positive Predictive Value Multilign(seed): 0.845 CMfinder(seed): 0.719 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.697 Afold: 0.589 Sensitivity Multilign(seed): 0.651 Afold: 0.592 Positive Predictive Value Multilign(seed): 0.747 Afold: 0.588 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	- HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.519 Multilign(seed): 0.485 Sensitivity HotKnots: 0.521 Multilign(seed): 0.386 Positive Predictive Value HotKnots: 0.526 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.94492482736e-08	+ Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.681 CRWrnafold: 0.453 Sensitivity Multilign(seed): 0.649 CRWrnafold: 0.465 Positive Predictive Value Multilign(seed): 0.717 CRWrnafold: 0.445 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	- Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.699 Multilign(seed): 0.485 Sensitivity Pknots: 0.684 Multilign(seed): 0.386 Positive Predictive Value Pknots: 0.721 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ Multilign(seed) vs McQFold Matthews Correlation Coefficient Multilign(seed): 0.681 McQFold: 0.509 Sensitivity Multilign(seed): 0.649 McQFold: 0.509 Positive Predictive Value Multilign(seed): 0.717 McQFold: 0.512 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.665 RNAshapes: 0.491 Sensitivity Multilign(seed): 0.632 RNAshapes: 0.502 Positive Predictive Value Multilign(seed): 0.701 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	- PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): 0.751 Multilign(seed): 0.698 Sensitivity PPfold(seed): 0.675 Multilign(seed): 0.660 Positive Predictive Value PPfold(seed): 0.838 Multilign(seed): 0.741 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Mastr(20) vs Multilign(seed) Matthews Correlation Coefficient Mastr(20): 0.775 Multilign(seed): 0.334 Sensitivity Mastr(20): 0.721 Multilign(seed): 0.186 Positive Predictive Value Mastr(20): 0.838 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.699 Murlet(seed): 0.656 Sensitivity Multilign(seed): 0.656 Murlet(seed): 0.480 Positive Predictive Value Multilign(seed): 0.746 Murlet(seed): 0.897 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.681 RNASLOpt: 0.478 Sensitivity Multilign(seed): 0.649 RNASLOpt: 0.457 Positive Predictive Value Multilign(seed): 0.717 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	- Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.766 Multilign(seed): 0.475 Sensitivity Cylofold: 0.719 Multilign(seed): 0.372 Positive Predictive Value Cylofold: 0.822 Multilign(seed): 0.617 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.34193807955e-08	+ Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.681 RNAwolf: 0.354 Sensitivity Multilign(seed): 0.649 RNAwolf: 0.368 Positive Predictive Value Multilign(seed): 0.717 RNAwolf: 0.342 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.681 Vsfold4: 0.205 Sensitivity Multilign(seed): 0.649 Vsfold4: 0.194 Positive Predictive Value Multilign(seed): 0.717 Vsfold4: 0.221 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.681 Vsfold5: 0.271 Sensitivity Multilign(seed): 0.649 Vsfold5: 0.271 Positive Predictive Value Multilign(seed): 0.717 Vsfold5: 0.273 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): 0.485 Alterna: 0.420 Sensitivity Multilign(seed): 0.386 Alterna: 0.391 Positive Predictive Value Multilign(seed): 0.619 Alterna: 0.462 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.485 RDfolder: 0.480 Sensitivity Multilign(seed): 0.386 RDfolder: 0.391 Positive Predictive Value Multilign(seed): 0.619 RDfolder: 0.600 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000665114514833	+ Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.698 Carnac(seed): 0.556 Sensitivity Multilign(seed): 0.660 Carnac(seed): 0.330 Positive Predictive Value Multilign(seed): 0.741 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.485 MCFold: 0.359 Sensitivity Multilign(seed): 0.386 MCFold: 0.419 Positive Predictive Value Multilign(seed): 0.619 MCFold: 0.319 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.53777893337e-08	+ Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.698 RSpredict(seed): 0.586 Sensitivity Multilign(seed): 0.660 RSpredict(seed): 0.477 Positive Predictive Value Multilign(seed): 0.741 RSpredict(seed): 0.722 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.720 NanoFolder: 0.328 Sensitivity Multilign(seed): 0.639 NanoFolder: 0.402 Positive Predictive Value Multilign(seed): 0.813 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.698 Mastr(seed): 0.491 Sensitivity Multilign(seed): 0.660 Mastr(seed): 0.299 Positive Predictive Value Multilign(seed): 0.741 Mastr(seed): 0.809 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08
MaxExpect	51 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.791 MaxExpect: 0.681 Sensitivity TurboFold(seed): 0.762 MaxExpect: 0.685 Positive Predictive Value TurboFold(seed): 0.822 MaxExpect: 0.679 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1224 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 MaxExpect: 0.514 Sensitivity PETfold_pre2.0(seed): 0.675 MaxExpect: 0.503 Positive Predictive Value PETfold_pre2.0(seed): 0.814 MaxExpect: 0.526 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.686 MaxExpect: 0.476 Sensitivity ContextFold: 0.648 MaxExpect: 0.465 Positive Predictive Value ContextFold: 0.725 MaxExpect: 0.488 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.787 MaxExpect: 0.622 Sensitivity TurboFold(20): 0.740 MaxExpect: 0.602 Positive Predictive Value TurboFold(20): 0.837 MaxExpect: 0.644 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 MaxExpect: 0.544 Sensitivity CentroidAlifold(seed): 0.623 MaxExpect: 0.529 Positive Predictive Value CentroidAlifold(seed): 0.901 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 MaxExpect: 0.512 Sensitivity PETfold_pre2.0(20): 0.686 MaxExpect: 0.498 Positive Predictive Value PETfold_pre2.0(20): 0.807 MaxExpect: 0.526 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.740 MaxExpect: 0.512 Sensitivity CentroidAlifold(20): 0.616 MaxExpect: 0.499 Positive Predictive Value CentroidAlifold(20): 0.891 MaxExpect: 0.527 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 MaxExpect: 0.562 Sensitivity CentroidHomfold‑LAST: 0.527 MaxExpect: 0.551 Positive Predictive Value CentroidHomfold‑LAST: 0.850 MaxExpect: 0.576 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.758 MaxExpect: 0.603 Sensitivity PPfold(20): 0.654 MaxExpect: 0.583 Positive Predictive Value PPfold(20): 0.879 MaxExpect: 0.625 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.687 MaxExpect: 0.512 Sensitivity RNAalifold(20): 0.600 MaxExpect: 0.499 Positive Predictive Value RNAalifold(20): 0.787 MaxExpect: 0.527 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	728 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.654 MaxExpect: 0.545 Sensitivity MXScarna(seed): 0.568 MaxExpect: 0.530 Positive Predictive Value MXScarna(seed): 0.753 MaxExpect: 0.561 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.647 MaxExpect: 0.512 Sensitivity MXScarna(20): 0.589 MaxExpect: 0.499 Positive Predictive Value MXScarna(20): 0.710 MaxExpect: 0.527 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1972 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.563 MaxExpect: 0.477 Sensitivity IPknot: 0.501 MaxExpect: 0.466 Positive Predictive Value IPknot: 0.632 MaxExpect: 0.489 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.685 MaxExpect: 0.624 Sensitivity Multilign(20): 0.617 MaxExpect: 0.604 Positive Predictive Value Multilign(20): 0.762 MaxExpect: 0.647 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 Murlet(20) vs MaxExpect Matthews Correlation Coefficient Murlet(20): 0.629 MaxExpect: 0.591 Sensitivity Murlet(20): 0.503 MaxExpect: 0.574 Positive Predictive Value Murlet(20): 0.787 MaxExpect: 0.610 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	700 RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.634 MaxExpect: 0.538 Sensitivity RNAalifold(seed): 0.482 MaxExpect: 0.523 Positive Predictive Value RNAalifold(seed): 0.835 MaxExpect: 0.553 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	1915 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.534 MaxExpect: 0.480 Sensitivity CentroidFold: 0.475 MaxExpect: 0.469 Positive Predictive Value CentroidFold: 0.600 MaxExpect: 0.492 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.676 MaxExpect: 0.624 Sensitivity RNASampler(20): 0.522 MaxExpect: 0.614 Positive Predictive Value RNASampler(20): 0.877 MaxExpect: 0.636 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.521 MaxExpect: 0.476 Sensitivity Contrafold: 0.506 MaxExpect: 0.465 Positive Predictive Value Contrafold: 0.537 MaxExpect: 0.488 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Sfold vs MaxExpect Matthews Correlation Coefficient Sfold: 0.481 MaxExpect: 0.476 Sensitivity Sfold: 0.433 MaxExpect: 0.465 Positive Predictive Value Sfold: 0.535 MaxExpect: 0.488 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.681 MaxExpect: 0.554 Sensitivity Multilign(seed): 0.649 MaxExpect: 0.562 Positive Predictive Value Multilign(seed): 0.717 MaxExpect: 0.548 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08		+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.476 ProbKnot: 0.471 Sensitivity MaxExpect: 0.465 ProbKnot: 0.468 Positive Predictive Value MaxExpect: 0.488 ProbKnot: 0.475 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.476 Fold: 0.448 Sensitivity MaxExpect: 0.465 Fold: 0.453 Positive Predictive Value MaxExpect: 0.488 Fold: 0.444 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.629 MaxExpect: 0.614 Sensitivity RNASampler(seed): 0.468 MaxExpect: 0.593 Positive Predictive Value RNASampler(seed): 0.847 MaxExpect: 0.639 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 9.291770879e-07	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.476 UNAFold: 0.447 Sensitivity MaxExpect: 0.465 UNAFold: 0.446 Positive Predictive Value MaxExpect: 0.488 UNAFold: 0.448 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.562 RNAsubopt: 0.525 Sensitivity MaxExpect: 0.551 RNAsubopt: 0.530 Positive Predictive Value MaxExpect: 0.576 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.512 RSpredict(20): 0.487 Sensitivity MaxExpect: 0.499 RSpredict(20): 0.402 Positive Predictive Value MaxExpect: 0.527 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.621 CMfinder(20): 0.549 Sensitivity MaxExpect: 0.601 CMfinder(20): 0.380 Positive Predictive Value MaxExpect: 0.644 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.500 PknotsRG: 0.466 Sensitivity MaxExpect: 0.487 PknotsRG: 0.467 Positive Predictive Value MaxExpect: 0.514 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs MaxExpect Matthews Correlation Coefficient Carnac(20): 0.518 MaxExpect: 0.512 Sensitivity Carnac(20): 0.301 MaxExpect: 0.499 Positive Predictive Value Carnac(20): 0.892 MaxExpect: 0.527 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 8.1815824276e-08	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.476 RNAfold: 0.440 Sensitivity MaxExpect: 0.465 RNAfold: 0.443 Positive Predictive Value MaxExpect: 0.488 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.594 CMfinder(seed): 0.486 Sensitivity MaxExpect: 0.583 CMfinder(seed): 0.312 Positive Predictive Value MaxExpect: 0.608 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.470 Afold: 0.434 Sensitivity MaxExpect: 0.457 Afold: 0.433 Positive Predictive Value MaxExpect: 0.484 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs HotKnots Matthews Correlation Coefficient MaxExpect: 0.634 HotKnots: 0.613 Sensitivity MaxExpect: 0.618 HotKnots: 0.607 Positive Predictive Value MaxExpect: 0.655 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.504 CRWrnafold: 0.437 Sensitivity MaxExpect: 0.491 CRWrnafold: 0.440 Positive Predictive Value MaxExpect: 0.518 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.640 Pknots: 0.606 Sensitivity MaxExpect: 0.621 Pknots: 0.595 Positive Predictive Value MaxExpect: 0.666 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.553 McQFold: 0.467 Sensitivity MaxExpect: 0.542 McQFold: 0.457 Positive Predictive Value MaxExpect: 0.565 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.565 RNAshapes: 0.477 Sensitivity MaxExpect: 0.552 RNAshapes: 0.472 Positive Predictive Value MaxExpect: 0.579 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.665 PPfold(seed): 0.626 Sensitivity MaxExpect: 0.670 PPfold(seed): 0.495 Positive Predictive Value MaxExpect: 0.662 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.533 Mastr(20): 0.296 Sensitivity MaxExpect: 0.521 Mastr(20): 0.111 Positive Predictive Value MaxExpect: 0.547 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.598 Murlet(seed): 0.540 Sensitivity MaxExpect: 0.585 Murlet(seed): 0.360 Positive Predictive Value MaxExpect: 0.613 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.566 RNASLOpt: 0.470 Sensitivity MaxExpect: 0.554 RNASLOpt: 0.442 Positive Predictive Value MaxExpect: 0.580 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.660 Cylofold: 0.575 Sensitivity MaxExpect: 0.642 Cylofold: 0.551 Positive Predictive Value MaxExpect: 0.683 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.526 RNAwolf: 0.343 Sensitivity MaxExpect: 0.513 RNAwolf: 0.358 Positive Predictive Value MaxExpect: 0.540 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.562 Vsfold4: 0.346 Sensitivity MaxExpect: 0.550 Vsfold4: 0.318 Positive Predictive Value MaxExpect: 0.576 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.563 Vsfold5: 0.339 Sensitivity MaxExpect: 0.551 Vsfold5: 0.322 Positive Predictive Value MaxExpect: 0.578 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.641 Alterna: 0.552 Sensitivity MaxExpect: 0.622 Alterna: 0.547 Positive Predictive Value MaxExpect: 0.667 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.641 RDfolder: 0.520 Sensitivity MaxExpect: 0.622 RDfolder: 0.464 Positive Predictive Value MaxExpect: 0.667 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.583 Carnac(seed): 0.244 Sensitivity MaxExpect: 0.579 Carnac(seed): 0.069 Positive Predictive Value MaxExpect: 0.588 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.642 MCFold: 0.473 Sensitivity MaxExpect: 0.623 MCFold: 0.524 Positive Predictive Value MaxExpect: 0.666 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.547 RSpredict(seed): 0.369 Sensitivity MaxExpect: 0.532 RSpredict(seed): 0.229 Positive Predictive Value MaxExpect: 0.563 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.586 NanoFolder: 0.194 Sensitivity MaxExpect: 0.570 NanoFolder: 0.229 Positive Predictive Value MaxExpect: 0.604 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.601 Mastr(seed): 0.113 Sensitivity MaxExpect: 0.587 Mastr(seed): 0.016 Positive Predictive Value MaxExpect: 0.618 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08
ProbKnot	51 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.791 ProbKnot: 0.684 Sensitivity TurboFold(seed): 0.762 ProbKnot: 0.691 Positive Predictive Value TurboFold(seed): 0.822 ProbKnot: 0.678 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1224 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 ProbKnot: 0.510 Sensitivity PETfold_pre2.0(seed): 0.675 ProbKnot: 0.506 Positive Predictive Value PETfold_pre2.0(seed): 0.814 ProbKnot: 0.516 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.686 ProbKnot: 0.471 Sensitivity ContextFold: 0.648 ProbKnot: 0.468 Positive Predictive Value ContextFold: 0.725 ProbKnot: 0.475 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.787 ProbKnot: 0.619 Sensitivity TurboFold(20): 0.740 ProbKnot: 0.604 Positive Predictive Value TurboFold(20): 0.837 ProbKnot: 0.637 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 ProbKnot: 0.540 Sensitivity CentroidAlifold(seed): 0.623 ProbKnot: 0.529 Positive Predictive Value CentroidAlifold(seed): 0.901 ProbKnot: 0.551 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 ProbKnot: 0.507 Sensitivity PETfold_pre2.0(20): 0.686 ProbKnot: 0.497 Positive Predictive Value PETfold_pre2.0(20): 0.807 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.740 ProbKnot: 0.507 Sensitivity CentroidAlifold(20): 0.616 ProbKnot: 0.498 Positive Predictive Value CentroidAlifold(20): 0.891 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 ProbKnot: 0.561 Sensitivity CentroidHomfold‑LAST: 0.527 ProbKnot: 0.556 Positive Predictive Value CentroidHomfold‑LAST: 0.850 ProbKnot: 0.567 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.758 ProbKnot: 0.601 Sensitivity PPfold(20): 0.654 ProbKnot: 0.585 Positive Predictive Value PPfold(20): 0.879 ProbKnot: 0.618 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.687 ProbKnot: 0.507 Sensitivity RNAalifold(20): 0.600 ProbKnot: 0.498 Positive Predictive Value RNAalifold(20): 0.787 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	728 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.654 ProbKnot: 0.541 Sensitivity MXScarna(seed): 0.568 ProbKnot: 0.530 Positive Predictive Value MXScarna(seed): 0.753 ProbKnot: 0.553 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.647 ProbKnot: 0.507 Sensitivity MXScarna(20): 0.589 ProbKnot: 0.498 Positive Predictive Value MXScarna(20): 0.710 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1972 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.563 ProbKnot: 0.472 Sensitivity IPknot: 0.501 ProbKnot: 0.469 Positive Predictive Value IPknot: 0.632 ProbKnot: 0.476 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.685 ProbKnot: 0.622 Sensitivity Multilign(20): 0.617 ProbKnot: 0.606 Positive Predictive Value Multilign(20): 0.762 ProbKnot: 0.640 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 Murlet(20) vs ProbKnot Matthews Correlation Coefficient Murlet(20): 0.629 ProbKnot: 0.588 Sensitivity Murlet(20): 0.503 ProbKnot: 0.576 Positive Predictive Value Murlet(20): 0.787 ProbKnot: 0.601 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	700 RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.634 ProbKnot: 0.534 Sensitivity RNAalifold(seed): 0.482 ProbKnot: 0.524 Positive Predictive Value RNAalifold(seed): 0.835 ProbKnot: 0.545 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	1915 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.534 ProbKnot: 0.475 Sensitivity CentroidFold: 0.475 ProbKnot: 0.473 Positive Predictive Value CentroidFold: 0.600 ProbKnot: 0.479 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.676 ProbKnot: 0.620 Sensitivity RNASampler(20): 0.522 ProbKnot: 0.617 Positive Predictive Value RNASampler(20): 0.877 ProbKnot: 0.624 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.521 ProbKnot: 0.471 Sensitivity Contrafold: 0.506 ProbKnot: 0.468 Positive Predictive Value Contrafold: 0.537 ProbKnot: 0.475 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.481 ProbKnot: 0.471 Sensitivity Sfold: 0.433 ProbKnot: 0.468 Positive Predictive Value Sfold: 0.535 ProbKnot: 0.475 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.681 ProbKnot: 0.566 Sensitivity Multilign(seed): 0.649 ProbKnot: 0.578 Positive Predictive Value Multilign(seed): 0.717 ProbKnot: 0.556 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	1973 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.476 ProbKnot: 0.471 Sensitivity MaxExpect: 0.465 ProbKnot: 0.468 Positive Predictive Value MaxExpect: 0.488 ProbKnot: 0.475 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.471 Fold: 0.448 Sensitivity ProbKnot: 0.468 Fold: 0.453 Positive Predictive Value ProbKnot: 0.475 Fold: 0.444 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.629 ProbKnot: 0.601 Sensitivity RNASampler(seed): 0.468 ProbKnot: 0.588 Positive Predictive Value RNASampler(seed): 0.847 ProbKnot: 0.618 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.471 UNAFold: 0.447 Sensitivity ProbKnot: 0.468 UNAFold: 0.446 Positive Predictive Value ProbKnot: 0.475 UNAFold: 0.448 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.561 RNAsubopt: 0.525 Sensitivity ProbKnot: 0.556 RNAsubopt: 0.530 Positive Predictive Value ProbKnot: 0.567 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.507 RSpredict(20): 0.487 Sensitivity ProbKnot: 0.498 RSpredict(20): 0.402 Positive Predictive Value ProbKnot: 0.517 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.619 CMfinder(20): 0.549 Sensitivity ProbKnot: 0.603 CMfinder(20): 0.380 Positive Predictive Value ProbKnot: 0.637 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs PknotsRG Matthews Correlation Coefficient ProbKnot: 0.496 PknotsRG: 0.466 Sensitivity ProbKnot: 0.492 PknotsRG: 0.467 Positive Predictive Value ProbKnot: 0.501 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs ProbKnot Matthews Correlation Coefficient Carnac(20): 0.518 ProbKnot: 0.507 Sensitivity Carnac(20): 0.301 ProbKnot: 0.498 Positive Predictive Value Carnac(20): 0.892 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.471 RNAfold: 0.440 Sensitivity ProbKnot: 0.468 RNAfold: 0.443 Positive Predictive Value ProbKnot: 0.475 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: 0.592 CMfinder(seed): 0.486 Sensitivity ProbKnot: 0.584 CMfinder(seed): 0.312 Positive Predictive Value ProbKnot: 0.601 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.464 Afold: 0.434 Sensitivity ProbKnot: 0.459 Afold: 0.433 Positive Predictive Value ProbKnot: 0.469 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs HotKnots Matthews Correlation Coefficient ProbKnot: 0.632 HotKnots: 0.613 Sensitivity ProbKnot: 0.623 HotKnots: 0.607 Positive Predictive Value ProbKnot: 0.645 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CRWrnafold Matthews Correlation Coefficient ProbKnot: 0.500 CRWrnafold: 0.437 Sensitivity ProbKnot: 0.497 CRWrnafold: 0.440 Positive Predictive Value ProbKnot: 0.505 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.639 Pknots: 0.606 Sensitivity ProbKnot: 0.631 Pknots: 0.595 Positive Predictive Value ProbKnot: 0.655 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.550 McQFold: 0.467 Sensitivity ProbKnot: 0.548 McQFold: 0.457 Positive Predictive Value ProbKnot: 0.553 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.563 RNAshapes: 0.477 Sensitivity ProbKnot: 0.558 RNAshapes: 0.472 Positive Predictive Value ProbKnot: 0.570 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.667 PPfold(seed): 0.626 Sensitivity ProbKnot: 0.679 PPfold(seed): 0.495 Positive Predictive Value ProbKnot: 0.656 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.529 Mastr(20): 0.296 Sensitivity ProbKnot: 0.522 Mastr(20): 0.111 Positive Predictive Value ProbKnot: 0.536 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.595 Murlet(seed): 0.540 Sensitivity ProbKnot: 0.588 Murlet(seed): 0.360 Positive Predictive Value ProbKnot: 0.604 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.564 RNASLOpt: 0.470 Sensitivity ProbKnot: 0.560 RNASLOpt: 0.442 Positive Predictive Value ProbKnot: 0.571 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.658 Cylofold: 0.575 Sensitivity ProbKnot: 0.649 Cylofold: 0.551 Positive Predictive Value ProbKnot: 0.673 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.522 RNAwolf: 0.343 Sensitivity ProbKnot: 0.520 RNAwolf: 0.358 Positive Predictive Value ProbKnot: 0.526 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.561 Vsfold4: 0.346 Sensitivity ProbKnot: 0.556 Vsfold4: 0.318 Positive Predictive Value ProbKnot: 0.567 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.562 Vsfold5: 0.339 Sensitivity ProbKnot: 0.557 Vsfold5: 0.322 Positive Predictive Value ProbKnot: 0.568 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.640 Alterna: 0.552 Sensitivity ProbKnot: 0.632 Alterna: 0.547 Positive Predictive Value ProbKnot: 0.656 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.640 RDfolder: 0.520 Sensitivity ProbKnot: 0.632 RDfolder: 0.464 Positive Predictive Value ProbKnot: 0.656 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.578 Carnac(seed): 0.244 Sensitivity ProbKnot: 0.579 Carnac(seed): 0.069 Positive Predictive Value ProbKnot: 0.579 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.639 MCFold: 0.473 Sensitivity ProbKnot: 0.628 MCFold: 0.524 Positive Predictive Value ProbKnot: 0.656 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.544 RSpredict(seed): 0.369 Sensitivity ProbKnot: 0.533 RSpredict(seed): 0.229 Positive Predictive Value ProbKnot: 0.555 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.585 NanoFolder: 0.194 Sensitivity ProbKnot: 0.577 NanoFolder: 0.229 Positive Predictive Value ProbKnot: 0.595 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.599 Mastr(seed): 0.113 Sensitivity ProbKnot: 0.590 Mastr(seed): 0.016 Positive Predictive Value ProbKnot: 0.610 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08
Fold	51 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.791 Fold: 0.678 Sensitivity TurboFold(seed): 0.762 Fold: 0.686 Positive Predictive Value TurboFold(seed): 0.822 Fold: 0.671 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1224 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 Fold: 0.490 Sensitivity PETfold_pre2.0(seed): 0.675 Fold: 0.493 Positive Predictive Value PETfold_pre2.0(seed): 0.814 Fold: 0.488 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.686 Fold: 0.448 Sensitivity ContextFold: 0.648 Fold: 0.453 Positive Predictive Value ContextFold: 0.725 Fold: 0.444 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.787 Fold: 0.599 Sensitivity TurboFold(20): 0.740 Fold: 0.593 Positive Predictive Value TurboFold(20): 0.837 Fold: 0.607 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 Fold: 0.519 Sensitivity CentroidAlifold(seed): 0.623 Fold: 0.518 Positive Predictive Value CentroidAlifold(seed): 0.901 Fold: 0.521 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 Fold: 0.485 Sensitivity PETfold_pre2.0(20): 0.686 Fold: 0.485 Positive Predictive Value PETfold_pre2.0(20): 0.807 Fold: 0.485 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 Fold: 0.485 Sensitivity CentroidAlifold(20): 0.616 Fold: 0.486 Positive Predictive Value CentroidAlifold(20): 0.891 Fold: 0.485 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 Fold: 0.543 Sensitivity CentroidHomfold‑LAST: 0.527 Fold: 0.545 Positive Predictive Value CentroidHomfold‑LAST: 0.850 Fold: 0.543 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.758 Fold: 0.580 Sensitivity PPfold(20): 0.654 Fold: 0.574 Positive Predictive Value PPfold(20): 0.879 Fold: 0.587 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.687 Fold: 0.485 Sensitivity RNAalifold(20): 0.600 Fold: 0.486 Positive Predictive Value RNAalifold(20): 0.787 Fold: 0.485 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	728 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.654 Fold: 0.520 Sensitivity MXScarna(seed): 0.568 Fold: 0.518 Positive Predictive Value MXScarna(seed): 0.753 Fold: 0.522 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.647 Fold: 0.485 Sensitivity MXScarna(20): 0.589 Fold: 0.486 Positive Predictive Value MXScarna(20): 0.710 Fold: 0.485 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1972 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.563 Fold: 0.449 Sensitivity IPknot: 0.501 Fold: 0.454 Positive Predictive Value IPknot: 0.632 Fold: 0.445 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.685 Fold: 0.601 Sensitivity Multilign(20): 0.617 Fold: 0.595 Positive Predictive Value Multilign(20): 0.762 Fold: 0.610 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.629 Fold: 0.571 Sensitivity Murlet(20): 0.503 Fold: 0.568 Positive Predictive Value Murlet(20): 0.787 Fold: 0.576 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	700 RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.634 Fold: 0.513 Sensitivity RNAalifold(seed): 0.482 Fold: 0.512 Positive Predictive Value RNAalifold(seed): 0.835 Fold: 0.515 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	1915 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.534 Fold: 0.453 Sensitivity CentroidFold: 0.475 Fold: 0.458 Positive Predictive Value CentroidFold: 0.600 Fold: 0.449 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.676 Fold: 0.622 Sensitivity RNASampler(20): 0.522 Fold: 0.623 Positive Predictive Value RNASampler(20): 0.877 Fold: 0.623 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.521 Fold: 0.448 Sensitivity Contrafold: 0.506 Fold: 0.453 Positive Predictive Value Contrafold: 0.537 Fold: 0.444 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.481 Fold: 0.448 Sensitivity Sfold: 0.433 Fold: 0.453 Positive Predictive Value Sfold: 0.535 Fold: 0.444 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.681 Fold: 0.550 Sensitivity Multilign(seed): 0.649 Fold: 0.561 Positive Predictive Value Multilign(seed): 0.717 Fold: 0.541 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	1973 MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.476 Fold: 0.448 Sensitivity MaxExpect: 0.465 Fold: 0.453 Positive Predictive Value MaxExpect: 0.488 Fold: 0.444 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.471 Fold: 0.448 Sensitivity ProbKnot: 0.468 Fold: 0.453 Positive Predictive Value ProbKnot: 0.475 Fold: 0.444 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.629 Fold: 0.601 Sensitivity RNASampler(seed): 0.468 Fold: 0.589 Positive Predictive Value RNASampler(seed): 0.847 Fold: 0.616 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.448 UNAFold: 0.447 Sensitivity Fold: 0.453 UNAFold: 0.446 Positive Predictive Value Fold: 0.444 UNAFold: 0.448 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 4.32815307575e-07	+ Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.543 RNAsubopt: 0.525 Sensitivity Fold: 0.545 RNAsubopt: 0.530 Positive Predictive Value Fold: 0.543 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RSpredict(20) vs Fold Matthews Correlation Coefficient RSpredict(20): 0.487 Fold: 0.485 Sensitivity RSpredict(20): 0.402 Fold: 0.486 Positive Predictive Value RSpredict(20): 0.590 Fold: 0.485 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 0.657358697881	+ Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.598 CMfinder(20): 0.549 Sensitivity Fold: 0.592 CMfinder(20): 0.380 Positive Predictive Value Fold: 0.606 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.474 PknotsRG: 0.466 Sensitivity Fold: 0.478 PknotsRG: 0.467 Positive Predictive Value Fold: 0.472 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs Fold Matthews Correlation Coefficient Carnac(20): 0.518 Fold: 0.485 Sensitivity Carnac(20): 0.301 Fold: 0.486 Positive Predictive Value Carnac(20): 0.892 Fold: 0.485 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.448 RNAfold: 0.440 Sensitivity Fold: 0.453 RNAfold: 0.443 Positive Predictive Value Fold: 0.444 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.590 CMfinder(seed): 0.486 Sensitivity Fold: 0.591 CMfinder(seed): 0.312 Positive Predictive Value Fold: 0.590 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.443 Afold: 0.434 Sensitivity Fold: 0.446 Afold: 0.433 Positive Predictive Value Fold: 0.440 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.630 HotKnots: 0.613 Sensitivity Fold: 0.622 HotKnots: 0.607 Positive Predictive Value Fold: 0.643 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CRWrnafold Matthews Correlation Coefficient Fold: 0.479 CRWrnafold: 0.437 Sensitivity Fold: 0.483 CRWrnafold: 0.440 Positive Predictive Value Fold: 0.477 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Pknots Matthews Correlation Coefficient Fold: 0.633 Pknots: 0.606 Sensitivity Fold: 0.622 Pknots: 0.595 Positive Predictive Value Fold: 0.650 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs McQFold Matthews Correlation Coefficient Fold: 0.531 McQFold: 0.467 Sensitivity Fold: 0.535 McQFold: 0.457 Positive Predictive Value Fold: 0.529 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.546 RNAshapes: 0.477 Sensitivity Fold: 0.547 RNAshapes: 0.472 Positive Predictive Value Fold: 0.547 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.657 PPfold(seed): 0.626 Sensitivity Fold: 0.667 PPfold(seed): 0.495 Positive Predictive Value Fold: 0.648 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.510 Mastr(20): 0.296 Sensitivity Fold: 0.512 Mastr(20): 0.111 Positive Predictive Value Fold: 0.509 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.586 Murlet(seed): 0.540 Sensitivity Fold: 0.583 Murlet(seed): 0.360 Positive Predictive Value Fold: 0.591 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.547 RNASLOpt: 0.470 Sensitivity Fold: 0.548 RNASLOpt: 0.442 Positive Predictive Value Fold: 0.548 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.654 Cylofold: 0.575 Sensitivity Fold: 0.644 Cylofold: 0.551 Positive Predictive Value Fold: 0.669 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.501 RNAwolf: 0.343 Sensitivity Fold: 0.504 RNAwolf: 0.358 Positive Predictive Value Fold: 0.498 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.544 Vsfold4: 0.346 Sensitivity Fold: 0.545 Vsfold4: 0.318 Positive Predictive Value Fold: 0.544 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.545 Vsfold5: 0.339 Sensitivity Fold: 0.546 Vsfold5: 0.322 Positive Predictive Value Fold: 0.545 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Alterna Matthews Correlation Coefficient Fold: 0.633 Alterna: 0.552 Sensitivity Fold: 0.623 Alterna: 0.547 Positive Predictive Value Fold: 0.650 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.633 RDfolder: 0.520 Sensitivity Fold: 0.623 RDfolder: 0.464 Positive Predictive Value Fold: 0.650 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.572 Carnac(seed): 0.244 Sensitivity Fold: 0.579 Carnac(seed): 0.069 Positive Predictive Value Fold: 0.567 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs MCFold Matthews Correlation Coefficient Fold: 0.635 MCFold: 0.473 Sensitivity Fold: 0.625 MCFold: 0.524 Positive Predictive Value Fold: 0.651 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.522 RSpredict(seed): 0.369 Sensitivity Fold: 0.521 RSpredict(seed): 0.229 Positive Predictive Value Fold: 0.524 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.557 NanoFolder: 0.194 Sensitivity Fold: 0.556 NanoFolder: 0.229 Positive Predictive Value Fold: 0.560 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.580 Mastr(seed): 0.113 Sensitivity Fold: 0.578 Mastr(seed): 0.016 Positive Predictive Value Fold: 0.582 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(seed)	31 TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): 0.825 RNASampler(seed): 0.722 Sensitivity TurboFold(seed): 0.771 RNASampler(seed): 0.582 Positive Predictive Value TurboFold(seed): 0.883 RNASampler(seed): 0.897 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.813 RNASampler(seed): 0.629 Sensitivity PETfold_pre2.0(seed): 0.728 RNASampler(seed): 0.468 Positive Predictive Value PETfold_pre2.0(seed): 0.910 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.692 RNASampler(seed): 0.629 Sensitivity ContextFold: 0.649 RNASampler(seed): 0.468 Positive Predictive Value ContextFold: 0.740 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.769 RNASampler(seed): 0.571 Sensitivity TurboFold(20): 0.707 RNASampler(seed): 0.343 Positive Predictive Value TurboFold(20): 0.841 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.852 RNASampler(seed): 0.629 Sensitivity CentroidAlifold(seed): 0.740 RNASampler(seed): 0.468 Positive Predictive Value CentroidAlifold(seed): 0.983 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 PETfold_pre2.0(20) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNASampler(seed): 0.571 Sensitivity PETfold_pre2.0(20): 0.627 RNASampler(seed): 0.343 Positive Predictive Value PETfold_pre2.0(20): 0.867 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 5.23657817852e-08	42 CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.822 RNASampler(seed): 0.571 Sensitivity CentroidAlifold(20): 0.739 RNASampler(seed): 0.343 Positive Predictive Value CentroidAlifold(20): 0.917 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.742 RNASampler(seed): 0.629 Sensitivity CentroidHomfold‑LAST: 0.664 RNASampler(seed): 0.468 Positive Predictive Value CentroidHomfold‑LAST: 0.831 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 PPfold(20) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(20): 0.690 RNASampler(seed): 0.571 Sensitivity PPfold(20): 0.547 RNASampler(seed): 0.343 Positive Predictive Value PPfold(20): 0.876 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 RNAalifold(20) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(20): 0.659 RNASampler(seed): 0.571 Sensitivity RNAalifold(20): 0.511 RNASampler(seed): 0.343 Positive Predictive Value RNAalifold(20): 0.857 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.738 RNASampler(seed): 0.629 Sensitivity MXScarna(seed): 0.703 RNASampler(seed): 0.468 Positive Predictive Value MXScarna(seed): 0.777 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 MXScarna(20) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(20): 0.835 RNASampler(seed): 0.571 Sensitivity MXScarna(20): 0.800 RNASampler(seed): 0.343 Positive Predictive Value MXScarna(20): 0.874 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.673 RNASampler(seed): 0.629 Sensitivity IPknot: 0.620 RNASampler(seed): 0.468 Positive Predictive Value IPknot: 0.732 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Multilign(20) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(20): 0.692 RNASampler(seed): 0.571 Sensitivity Multilign(20): 0.552 RNASampler(seed): 0.343 Positive Predictive Value Multilign(20): 0.874 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Murlet(20) vs RNASampler(seed) Matthews Correlation Coefficient Murlet(20): 0.685 RNASampler(seed): 0.571 Sensitivity Murlet(20): 0.527 RNASampler(seed): 0.343 Positive Predictive Value Murlet(20): 0.896 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNAalifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.736 RNASampler(seed): 0.629 Sensitivity RNAalifold(seed): 0.594 RNASampler(seed): 0.468 Positive Predictive Value RNAalifold(seed): 0.913 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.646 RNASampler(seed): 0.629 Sensitivity CentroidFold: 0.570 RNASampler(seed): 0.468 Positive Predictive Value CentroidFold: 0.735 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): 0.640 RNASampler(seed): 0.571 Sensitivity RNASampler(20): 0.454 RNASampler(seed): 0.343 Positive Predictive Value RNASampler(20): 0.909 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.639 RNASampler(seed): 0.629 Sensitivity Contrafold: 0.603 RNASampler(seed): 0.468 Positive Predictive Value Contrafold: 0.679 RNASampler(seed): 0.847 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 2.82781450476e-07	98 RNASampler(seed) vs Sfold Matthews Correlation Coefficient RNASampler(seed): 0.629 Sfold: 0.603 Sensitivity RNASampler(seed): 0.468 Sfold: 0.554 Positive Predictive Value RNASampler(seed): 0.847 Sfold: 0.659 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.753 RNASampler(seed): 0.702 Sensitivity Multilign(seed): 0.684 RNASampler(seed): 0.572 Positive Predictive Value Multilign(seed): 0.830 RNASampler(seed): 0.864 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.7968284078e-08	98 RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.629 MaxExpect: 0.614 Sensitivity RNASampler(seed): 0.468 MaxExpect: 0.593 Positive Predictive Value RNASampler(seed): 0.847 MaxExpect: 0.639 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 9.291770879e-07	98 RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.629 ProbKnot: 0.601 Sensitivity RNASampler(seed): 0.468 ProbKnot: 0.588 Positive Predictive Value RNASampler(seed): 0.847 ProbKnot: 0.618 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.629 Fold: 0.601 Sensitivity RNASampler(seed): 0.468 Fold: 0.589 Positive Predictive Value RNASampler(seed): 0.847 Fold: 0.616 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.629 UNAFold: 0.612 Sensitivity RNASampler(seed): 0.468 UNAFold: 0.596 Positive Predictive Value RNASampler(seed): 0.847 UNAFold: 0.630 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 4.98094999346e-07	+ RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.629 RNAsubopt: 0.576 Sensitivity RNASampler(seed): 0.468 RNAsubopt: 0.567 Positive Predictive Value RNASampler(seed): 0.847 RNAsubopt: 0.589 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RSpredict(20) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(20): 0.753 RNASampler(seed): 0.571 Sensitivity RSpredict(20): 0.684 RNASampler(seed): 0.343 Positive Predictive Value RSpredict(20): 0.833 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 5.23657817852e-08	- CMfinder(20) vs RNASampler(seed) Matthews Correlation Coefficient CMfinder(20): 0.735 RNASampler(seed): 0.571 Sensitivity CMfinder(20): 0.607 RNASampler(seed): 0.343 Positive Predictive Value CMfinder(20): 0.894 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASampler(seed) vs PknotsRG Matthews Correlation Coefficient RNASampler(seed): 0.629 PknotsRG: 0.627 Sensitivity RNASampler(seed): 0.468 PknotsRG: 0.619 Positive Predictive Value RNASampler(seed): 0.847 PknotsRG: 0.637 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 0.657358697881	+ RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.571 Carnac(20): 0.461 Sensitivity RNASampler(seed): 0.343 Carnac(20): 0.241 Positive Predictive Value RNASampler(seed): 0.957 Carnac(20): 0.893 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): 0.629 RNAfold: 0.609 Sensitivity RNASampler(seed): 0.468 RNAfold: 0.594 Positive Predictive Value RNASampler(seed): 0.847 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): 0.631 CMfinder(seed): 0.560 Sensitivity RNASampler(seed): 0.472 CMfinder(seed): 0.424 Positive Predictive Value RNASampler(seed): 0.845 CMfinder(seed): 0.743 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.634 Afold: 0.602 Sensitivity RNASampler(seed): 0.471 Afold: 0.593 Positive Predictive Value RNASampler(seed): 0.856 Afold: 0.615 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.537 HotKnots: 0.536 Sensitivity RNASampler(seed): 0.372 HotKnots: 0.524 Positive Predictive Value RNASampler(seed): 0.780 HotKnots: 0.553 Number of pairs reference - predicted secondary structure: 84 Wilcoxon single-rank test P-value: 1.0	+ RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.629 CRWrnafold: 0.473 Sensitivity RNASampler(seed): 0.468 CRWrnafold: 0.465 Positive Predictive Value RNASampler(seed): 0.847 CRWrnafold: 0.485 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): 0.455 Pknots: 0.446 Sensitivity RNASampler(seed): 0.284 Pknots: 0.429 Positive Predictive Value RNASampler(seed): 0.738 Pknots: 0.475 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 2.71856013146e-06	+ RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.629 McQFold: 0.524 Sensitivity RNASampler(seed): 0.468 McQFold: 0.496 Positive Predictive Value RNASampler(seed): 0.847 McQFold: 0.557 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.623 RNAshapes: 0.555 Sensitivity RNASampler(seed): 0.461 RNAshapes: 0.544 Positive Predictive Value RNASampler(seed): 0.844 RNAshapes: 0.569 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(seed): 0.862 RNASampler(seed): 0.713 Sensitivity PPfold(seed): 0.777 RNASampler(seed): 0.571 Positive Predictive Value PPfold(seed): 0.957 RNASampler(seed): 0.890 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	- Mastr(20) vs RNASampler(seed) Matthews Correlation Coefficient Mastr(20): 0.773 RNASampler(seed): 0.571 Sensitivity Mastr(20): 0.712 RNASampler(seed): 0.343 Positive Predictive Value Mastr(20): 0.843 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.629 Murlet(seed): 0.572 Sensitivity RNASampler(seed): 0.468 Murlet(seed): 0.369 Positive Predictive Value RNASampler(seed): 0.847 Murlet(seed): 0.889 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): 0.629 RNASLOpt: 0.531 Sensitivity RNASampler(seed): 0.468 RNASLOpt: 0.485 Positive Predictive Value RNASampler(seed): 0.847 RNASLOpt: 0.585 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Cylofold Matthews Correlation Coefficient RNASampler(seed): 0.514 Cylofold: 0.503 Sensitivity RNASampler(seed): 0.335 Cylofold: 0.455 Positive Predictive Value RNASampler(seed): 0.797 Cylofold: 0.565 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 1.80472700427e-05	+ RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.629 RNAwolf: 0.354 Sensitivity RNASampler(seed): 0.468 RNAwolf: 0.360 Positive Predictive Value RNASampler(seed): 0.847 RNAwolf: 0.352 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.629 Vsfold4: 0.349 Sensitivity RNASampler(seed): 0.468 Vsfold4: 0.318 Positive Predictive Value RNASampler(seed): 0.847 Vsfold4: 0.388 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.629 Vsfold5: 0.357 Sensitivity RNASampler(seed): 0.468 Vsfold5: 0.340 Positive Predictive Value RNASampler(seed): 0.847 Vsfold5: 0.379 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): 0.455 Alterna: 0.449 Sensitivity RNASampler(seed): 0.284 Alterna: 0.422 Positive Predictive Value RNASampler(seed): 0.738 Alterna: 0.490 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 0.0716817872326	+ RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.455 RDfolder: 0.357 Sensitivity RNASampler(seed): 0.284 RDfolder: 0.288 Positive Predictive Value RNASampler(seed): 0.738 RDfolder: 0.456 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.629 Carnac(seed): 0.520 Sensitivity RNASampler(seed): 0.468 Carnac(seed): 0.310 Positive Predictive Value RNASampler(seed): 0.847 Carnac(seed): 0.874 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.502 MCFold: 0.422 Sensitivity RNASampler(seed): 0.334 MCFold: 0.464 Positive Predictive Value RNASampler(seed): 0.760 MCFold: 0.391 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.629 RSpredict(seed): 0.607 Sensitivity RNASampler(seed): 0.468 RSpredict(seed): 0.495 Positive Predictive Value RNASampler(seed): 0.847 RSpredict(seed): 0.747 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.526 NanoFolder: 0.315 Sensitivity RNASampler(seed): 0.356 NanoFolder: 0.382 Positive Predictive Value RNASampler(seed): 0.782 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.66763272401e-08	+ RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.629 Mastr(seed): 0.512 Sensitivity RNASampler(seed): 0.468 Mastr(seed): 0.322 Positive Predictive Value RNASampler(seed): 0.847 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08
UNAFold	51 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.791 UNAFold: 0.678 Sensitivity TurboFold(seed): 0.762 UNAFold: 0.680 Positive Predictive Value TurboFold(seed): 0.822 UNAFold: 0.679 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1224 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 UNAFold: 0.492 Sensitivity PETfold_pre2.0(seed): 0.675 UNAFold: 0.488 Positive Predictive Value PETfold_pre2.0(seed): 0.814 UNAFold: 0.496 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	1987 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.680 UNAFold: 0.445 Sensitivity ContextFold: 0.644 UNAFold: 0.445 Positive Predictive Value ContextFold: 0.718 UNAFold: 0.446 Number of pairs reference - predicted secondary structure: 1987 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.787 UNAFold: 0.587 Sensitivity TurboFold(20): 0.740 UNAFold: 0.575 Positive Predictive Value TurboFold(20): 0.837 UNAFold: 0.600 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 UNAFold: 0.536 Sensitivity CentroidAlifold(seed): 0.623 UNAFold: 0.528 Positive Predictive Value CentroidAlifold(seed): 0.901 UNAFold: 0.546 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 UNAFold: 0.496 Sensitivity PETfold_pre2.0(20): 0.686 UNAFold: 0.490 Positive Predictive Value PETfold_pre2.0(20): 0.807 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 UNAFold: 0.497 Sensitivity CentroidAlifold(20): 0.616 UNAFold: 0.491 Positive Predictive Value CentroidAlifold(20): 0.891 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 UNAFold: 0.533 Sensitivity CentroidHomfold‑LAST: 0.527 UNAFold: 0.528 Positive Predictive Value CentroidHomfold‑LAST: 0.850 UNAFold: 0.539 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.758 UNAFold: 0.575 Sensitivity PPfold(20): 0.654 UNAFold: 0.563 Positive Predictive Value PPfold(20): 0.879 UNAFold: 0.588 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.687 UNAFold: 0.497 Sensitivity RNAalifold(20): 0.600 UNAFold: 0.491 Positive Predictive Value RNAalifold(20): 0.787 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	728 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.654 UNAFold: 0.536 Sensitivity MXScarna(seed): 0.568 UNAFold: 0.528 Positive Predictive Value MXScarna(seed): 0.753 UNAFold: 0.546 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.647 UNAFold: 0.497 Sensitivity MXScarna(20): 0.589 UNAFold: 0.491 Positive Predictive Value MXScarna(20): 0.710 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1972 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.563 UNAFold: 0.447 Sensitivity IPknot: 0.501 UNAFold: 0.446 Positive Predictive Value IPknot: 0.632 UNAFold: 0.449 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.685 UNAFold: 0.591 Sensitivity Multilign(20): 0.617 UNAFold: 0.579 Positive Predictive Value Multilign(20): 0.762 UNAFold: 0.605 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.629 UNAFold: 0.563 Sensitivity Murlet(20): 0.503 UNAFold: 0.554 Positive Predictive Value Murlet(20): 0.787 UNAFold: 0.573 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	700 RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.634 UNAFold: 0.531 Sensitivity RNAalifold(seed): 0.482 UNAFold: 0.523 Positive Predictive Value RNAalifold(seed): 0.835 UNAFold: 0.540 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	1915 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.534 UNAFold: 0.454 Sensitivity CentroidFold: 0.475 UNAFold: 0.453 Positive Predictive Value CentroidFold: 0.600 UNAFold: 0.455 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.676 UNAFold: 0.598 Sensitivity RNASampler(20): 0.522 UNAFold: 0.591 Positive Predictive Value RNASampler(20): 0.877 UNAFold: 0.606 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.521 UNAFold: 0.447 Sensitivity Contrafold: 0.506 UNAFold: 0.446 Positive Predictive Value Contrafold: 0.537 UNAFold: 0.448 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.481 UNAFold: 0.447 Sensitivity Sfold: 0.433 UNAFold: 0.446 Positive Predictive Value Sfold: 0.535 UNAFold: 0.448 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.681 UNAFold: 0.543 Sensitivity Multilign(seed): 0.649 UNAFold: 0.552 Positive Predictive Value Multilign(seed): 0.717 UNAFold: 0.537 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	1973 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.476 UNAFold: 0.447 Sensitivity MaxExpect: 0.465 UNAFold: 0.446 Positive Predictive Value MaxExpect: 0.488 UNAFold: 0.448 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.471 UNAFold: 0.447 Sensitivity ProbKnot: 0.468 UNAFold: 0.446 Positive Predictive Value ProbKnot: 0.475 UNAFold: 0.448 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.448 UNAFold: 0.447 Sensitivity Fold: 0.453 UNAFold: 0.446 Positive Predictive Value Fold: 0.444 UNAFold: 0.448 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 4.32815307575e-07	98 RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.629 UNAFold: 0.612 Sensitivity RNASampler(seed): 0.468 UNAFold: 0.596 Positive Predictive Value RNASampler(seed): 0.847 UNAFold: 0.630 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 4.98094999346e-07		+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.533 RNAsubopt: 0.525 Sensitivity UNAFold: 0.528 RNAsubopt: 0.530 Positive Predictive Value UNAFold: 0.539 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.497 RSpredict(20): 0.487 Sensitivity UNAFold: 0.491 RSpredict(20): 0.402 Positive Predictive Value UNAFold: 0.503 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 1.97386617324e-07	+ UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.586 CMfinder(20): 0.549 Sensitivity UNAFold: 0.574 CMfinder(20): 0.380 Positive Predictive Value UNAFold: 0.600 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.474 PknotsRG: 0.466 Sensitivity UNAFold: 0.471 PknotsRG: 0.467 Positive Predictive Value UNAFold: 0.478 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.518 UNAFold: 0.497 Sensitivity Carnac(20): 0.301 UNAFold: 0.491 Positive Predictive Value Carnac(20): 0.892 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.447 RNAfold: 0.440 Sensitivity UNAFold: 0.446 RNAfold: 0.443 Positive Predictive Value UNAFold: 0.448 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.610 CMfinder(seed): 0.486 Sensitivity UNAFold: 0.602 CMfinder(seed): 0.312 Positive Predictive Value UNAFold: 0.620 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.446 Afold: 0.434 Sensitivity UNAFold: 0.444 Afold: 0.433 Positive Predictive Value UNAFold: 0.450 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.618 HotKnots: 0.613 Sensitivity UNAFold: 0.603 HotKnots: 0.607 Positive Predictive Value UNAFold: 0.638 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.477 CRWrnafold: 0.437 Sensitivity UNAFold: 0.474 CRWrnafold: 0.440 Positive Predictive Value UNAFold: 0.481 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs UNAFold Matthews Correlation Coefficient Pknots: 0.606 UNAFold: 0.596 Sensitivity Pknots: 0.595 UNAFold: 0.583 Positive Predictive Value Pknots: 0.624 UNAFold: 0.616 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.522 McQFold: 0.467 Sensitivity UNAFold: 0.519 McQFold: 0.457 Positive Predictive Value UNAFold: 0.526 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.534 RNAshapes: 0.477 Sensitivity UNAFold: 0.528 RNAshapes: 0.472 Positive Predictive Value UNAFold: 0.541 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.653 PPfold(seed): 0.626 Sensitivity UNAFold: 0.657 PPfold(seed): 0.495 Positive Predictive Value UNAFold: 0.651 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.500 Mastr(20): 0.296 Sensitivity UNAFold: 0.496 Mastr(20): 0.111 Positive Predictive Value UNAFold: 0.505 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.600 Murlet(seed): 0.540 Sensitivity UNAFold: 0.593 Murlet(seed): 0.360 Positive Predictive Value UNAFold: 0.609 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.535 RNASLOpt: 0.470 Sensitivity UNAFold: 0.530 RNASLOpt: 0.442 Positive Predictive Value UNAFold: 0.543 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.639 Cylofold: 0.575 Sensitivity UNAFold: 0.624 Cylofold: 0.551 Positive Predictive Value UNAFold: 0.661 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.492 RNAwolf: 0.343 Sensitivity UNAFold: 0.489 RNAwolf: 0.358 Positive Predictive Value UNAFold: 0.496 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.532 Vsfold4: 0.346 Sensitivity UNAFold: 0.527 Vsfold4: 0.318 Positive Predictive Value UNAFold: 0.539 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.532 Vsfold5: 0.339 Sensitivity UNAFold: 0.527 Vsfold5: 0.322 Positive Predictive Value UNAFold: 0.540 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.597 Alterna: 0.552 Sensitivity UNAFold: 0.584 Alterna: 0.547 Positive Predictive Value UNAFold: 0.617 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.597 RDfolder: 0.520 Sensitivity UNAFold: 0.584 RDfolder: 0.464 Positive Predictive Value UNAFold: 0.617 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.593 Carnac(seed): 0.244 Sensitivity UNAFold: 0.590 Carnac(seed): 0.069 Positive Predictive Value UNAFold: 0.597 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.618 MCFold: 0.473 Sensitivity UNAFold: 0.601 MCFold: 0.524 Positive Predictive Value UNAFold: 0.640 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.539 RSpredict(seed): 0.369 Sensitivity UNAFold: 0.530 RSpredict(seed): 0.229 Positive Predictive Value UNAFold: 0.548 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.556 NanoFolder: 0.194 Sensitivity UNAFold: 0.549 NanoFolder: 0.229 Positive Predictive Value UNAFold: 0.566 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.582 Mastr(seed): 0.113 Sensitivity UNAFold: 0.574 Mastr(seed): 0.016 Positive Predictive Value UNAFold: 0.592 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAsubopt	50 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.785 RNAsubopt: 0.640 Sensitivity TurboFold(seed): 0.758 RNAsubopt: 0.647 Positive Predictive Value TurboFold(seed): 0.814 RNAsubopt: 0.636 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	1128 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.733 RNAsubopt: 0.523 Sensitivity PETfold_pre2.0(seed): 0.652 RNAsubopt: 0.530 Positive Predictive Value PETfold_pre2.0(seed): 0.827 RNAsubopt: 0.518 Number of pairs reference - predicted secondary structure: 1128 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.749 RNAsubopt: 0.525 Sensitivity ContextFold: 0.712 RNAsubopt: 0.530 Positive Predictive Value ContextFold: 0.789 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.787 RNAsubopt: 0.570 Sensitivity TurboFold(20): 0.740 RNAsubopt: 0.570 Positive Predictive Value TurboFold(20): 0.837 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	629 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 RNAsubopt: 0.570 Sensitivity CentroidAlifold(seed): 0.577 RNAsubopt: 0.571 Positive Predictive Value CentroidAlifold(seed): 0.905 RNAsubopt: 0.570 Number of pairs reference - predicted secondary structure: 629 Wilcoxon single-rank test P-value: 3.56938820447e-08	562 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 RNAsubopt: 0.571 Sensitivity PETfold_pre2.0(20): 0.675 RNAsubopt: 0.570 Positive Predictive Value PETfold_pre2.0(20): 0.870 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 562 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.757 RNAsubopt: 0.570 Sensitivity CentroidAlifold(20): 0.618 RNAsubopt: 0.570 Positive Predictive Value CentroidAlifold(20): 0.928 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 RNAsubopt: 0.525 Sensitivity CentroidHomfold‑LAST: 0.527 RNAsubopt: 0.530 Positive Predictive Value CentroidHomfold‑LAST: 0.850 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	552 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.759 RNAsubopt: 0.570 Sensitivity PPfold(20): 0.652 RNAsubopt: 0.569 Positive Predictive Value PPfold(20): 0.885 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.705 RNAsubopt: 0.570 Sensitivity RNAalifold(20): 0.577 RNAsubopt: 0.570 Positive Predictive Value RNAalifold(20): 0.863 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	651 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.655 RNAsubopt: 0.570 Sensitivity MXScarna(seed): 0.561 RNAsubopt: 0.571 Positive Predictive Value MXScarna(seed): 0.766 RNAsubopt: 0.571 Number of pairs reference - predicted secondary structure: 651 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.701 RNAsubopt: 0.570 Sensitivity MXScarna(20): 0.634 RNAsubopt: 0.570 Positive Predictive Value MXScarna(20): 0.776 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.635 RNAsubopt: 0.525 Sensitivity IPknot: 0.588 RNAsubopt: 0.530 Positive Predictive Value IPknot: 0.688 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.685 RNAsubopt: 0.571 Sensitivity Multilign(20): 0.617 RNAsubopt: 0.570 Positive Predictive Value Multilign(20): 0.762 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	495 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.631 RNAsubopt: 0.573 Sensitivity Murlet(20): 0.496 RNAsubopt: 0.573 Positive Predictive Value Murlet(20): 0.803 RNAsubopt: 0.575 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	619 RNAsubopt vs RNAalifold(seed) Matthews Correlation Coefficient RNAsubopt: 0.569 RNAalifold(seed): 0.549 Sensitivity RNAsubopt: 0.570 RNAalifold(seed): 0.352 Positive Predictive Value RNAsubopt: 0.570 RNAalifold(seed): 0.859 Number of pairs reference - predicted secondary structure: 619 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.602 RNAsubopt: 0.525 Sensitivity CentroidFold: 0.555 RNAsubopt: 0.530 Positive Predictive Value CentroidFold: 0.653 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.676 RNAsubopt: 0.583 Sensitivity RNASampler(20): 0.522 RNAsubopt: 0.587 Positive Predictive Value RNASampler(20): 0.877 RNAsubopt: 0.580 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.588 RNAsubopt: 0.525 Sensitivity Contrafold: 0.578 RNAsubopt: 0.530 Positive Predictive Value Contrafold: 0.600 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.562 RNAsubopt: 0.525 Sensitivity Sfold: 0.516 RNAsubopt: 0.530 Positive Predictive Value Sfold: 0.614 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.681 RNAsubopt: 0.557 Sensitivity Multilign(seed): 0.649 RNAsubopt: 0.569 Positive Predictive Value Multilign(seed): 0.717 RNAsubopt: 0.548 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	1641 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.562 RNAsubopt: 0.525 Sensitivity MaxExpect: 0.551 RNAsubopt: 0.530 Positive Predictive Value MaxExpect: 0.576 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.561 RNAsubopt: 0.525 Sensitivity ProbKnot: 0.556 RNAsubopt: 0.530 Positive Predictive Value ProbKnot: 0.567 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.543 RNAsubopt: 0.525 Sensitivity Fold: 0.545 RNAsubopt: 0.530 Positive Predictive Value Fold: 0.543 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.629 RNAsubopt: 0.576 Sensitivity RNASampler(seed): 0.468 RNAsubopt: 0.567 Positive Predictive Value RNASampler(seed): 0.847 RNAsubopt: 0.589 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.533 RNAsubopt: 0.525 Sensitivity UNAFold: 0.528 RNAsubopt: 0.530 Positive Predictive Value UNAFold: 0.539 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.570 RSpredict(20): 0.524 Sensitivity RNAsubopt: 0.570 RSpredict(20): 0.385 Positive Predictive Value RNAsubopt: 0.573 RSpredict(20): 0.714 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.569 CMfinder(20): 0.549 Sensitivity RNAsubopt: 0.568 CMfinder(20): 0.380 Positive Predictive Value RNAsubopt: 0.572 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.530 RNAsubopt: 0.525 Sensitivity PknotsRG: 0.530 RNAsubopt: 0.530 Positive Predictive Value PknotsRG: 0.531 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Carnac(20) Matthews Correlation Coefficient RNAsubopt: 0.570 Carnac(20): 0.469 Sensitivity RNAsubopt: 0.570 Carnac(20): 0.248 Positive Predictive Value RNAsubopt: 0.573 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.531 RNAsubopt: 0.525 Sensitivity RNAfold: 0.531 RNAsubopt: 0.530 Positive Predictive Value RNAfold: 0.533 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs CMfinder(seed) Matthews Correlation Coefficient RNAsubopt: 0.585 CMfinder(seed): 0.486 Sensitivity RNAsubopt: 0.587 CMfinder(seed): 0.312 Positive Predictive Value RNAsubopt: 0.584 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.553 Afold: 0.537 Sensitivity RNAsubopt: 0.553 Afold: 0.531 Positive Predictive Value RNAsubopt: 0.554 Afold: 0.545 Number of pairs reference - predicted secondary structure: 1002 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs HotKnots Matthews Correlation Coefficient RNAsubopt: 0.615 HotKnots: 0.613 Sensitivity RNAsubopt: 0.609 HotKnots: 0.607 Positive Predictive Value RNAsubopt: 0.626 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 7.14263132478e-06	+ RNAsubopt vs CRWrnafold Matthews Correlation Coefficient RNAsubopt: 0.525 CRWrnafold: 0.480 Sensitivity RNAsubopt: 0.530 CRWrnafold: 0.481 Positive Predictive Value RNAsubopt: 0.521 CRWrnafold: 0.482 Number of pairs reference - predicted secondary structure: 1640 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.608 Pknots: 0.606 Sensitivity RNAsubopt: 0.602 Pknots: 0.595 Positive Predictive Value RNAsubopt: 0.620 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 0.028456752624	+ RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.525 McQFold: 0.479 Sensitivity RNAsubopt: 0.530 McQFold: 0.466 Positive Predictive Value RNAsubopt: 0.521 McQFold: 0.494 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.526 RNAshapes: 0.477 Sensitivity RNAsubopt: 0.531 RNAshapes: 0.472 Positive Predictive Value RNAsubopt: 0.523 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.668 PPfold(seed): 0.635 Sensitivity RNAsubopt: 0.679 PPfold(seed): 0.511 Positive Predictive Value RNAsubopt: 0.660 PPfold(seed): 0.790 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.570 Mastr(20): 0.350 Sensitivity RNAsubopt: 0.570 Mastr(20): 0.156 Positive Predictive Value RNAsubopt: 0.573 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.595 Murlet(seed): 0.519 Sensitivity RNAsubopt: 0.594 Murlet(seed): 0.322 Positive Predictive Value RNAsubopt: 0.597 Murlet(seed): 0.839 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.529 RNASLOpt: 0.471 Sensitivity RNAsubopt: 0.534 RNASLOpt: 0.444 Positive Predictive Value RNAsubopt: 0.526 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1542 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.639 Cylofold: 0.575 Sensitivity RNAsubopt: 0.631 Cylofold: 0.551 Positive Predictive Value RNAsubopt: 0.652 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.525 RNAwolf: 0.384 Sensitivity RNAsubopt: 0.530 RNAwolf: 0.397 Positive Predictive Value RNAsubopt: 0.521 RNAwolf: 0.373 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.525 Vsfold4: 0.346 Sensitivity RNAsubopt: 0.530 Vsfold4: 0.318 Positive Predictive Value RNAsubopt: 0.521 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.525 Vsfold5: 0.339 Sensitivity RNAsubopt: 0.530 Vsfold5: 0.322 Positive Predictive Value RNAsubopt: 0.521 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.608 Alterna: 0.552 Sensitivity RNAsubopt: 0.603 Alterna: 0.547 Positive Predictive Value RNAsubopt: 0.621 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.608 RDfolder: 0.520 Sensitivity RNAsubopt: 0.603 RDfolder: 0.464 Positive Predictive Value RNAsubopt: 0.621 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.570 Carnac(seed): 0.224 Sensitivity RNAsubopt: 0.577 Carnac(seed): 0.057 Positive Predictive Value RNAsubopt: 0.564 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.619 MCFold: 0.473 Sensitivity RNAsubopt: 0.610 MCFold: 0.524 Positive Predictive Value RNAsubopt: 0.633 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.570 RSpredict(seed): 0.236 Sensitivity RNAsubopt: 0.571 RSpredict(seed): 0.105 Positive Predictive Value RNAsubopt: 0.570 RSpredict(seed): 0.530 Number of pairs reference - predicted secondary structure: 632 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.547 NanoFolder: 0.198 Sensitivity RNAsubopt: 0.551 NanoFolder: 0.233 Positive Predictive Value RNAsubopt: 0.546 NanoFolder: 0.171 Number of pairs reference - predicted secondary structure: 248 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.573 Mastr(seed): 0.117 Sensitivity RNAsubopt: 0.575 Mastr(seed): 0.017 Positive Predictive Value RNAsubopt: 0.572 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 628 Wilcoxon single-rank test P-value: 3.56938820447e-08
RSpredict(20)	19 TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 RSpredict(20): 0.758 Sensitivity TurboFold(seed): 0.851 RSpredict(20): 0.651 Positive Predictive Value TurboFold(seed): 0.867 RSpredict(20): 0.885 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.08932646657e-08	626 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 RSpredict(20): 0.483 Sensitivity PETfold_pre2.0(seed): 0.729 RSpredict(20): 0.398 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RSpredict(20): 0.587 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.791 RSpredict(20): 0.487 Sensitivity ContextFold: 0.752 RSpredict(20): 0.402 Positive Predictive Value ContextFold: 0.832 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.787 RSpredict(20): 0.524 Sensitivity TurboFold(20): 0.740 RSpredict(20): 0.385 Positive Predictive Value TurboFold(20): 0.837 RSpredict(20): 0.714 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 RSpredict(20): 0.532 Sensitivity CentroidAlifold(seed): 0.652 RSpredict(20): 0.425 Positive Predictive Value CentroidAlifold(seed): 0.918 RSpredict(20): 0.666 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 RSpredict(20): 0.487 Sensitivity PETfold_pre2.0(20): 0.686 RSpredict(20): 0.402 Positive Predictive Value PETfold_pre2.0(20): 0.807 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.740 RSpredict(20): 0.487 Sensitivity CentroidAlifold(20): 0.616 RSpredict(20): 0.402 Positive Predictive Value CentroidAlifold(20): 0.891 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 RSpredict(20): 0.524 Sensitivity CentroidHomfold‑LAST: 0.625 RSpredict(20): 0.385 Positive Predictive Value CentroidHomfold‑LAST: 0.899 RSpredict(20): 0.714 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.758 RSpredict(20): 0.526 Sensitivity PPfold(20): 0.654 RSpredict(20): 0.396 Positive Predictive Value PPfold(20): 0.879 RSpredict(20): 0.699 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.687 RSpredict(20): 0.487 Sensitivity RNAalifold(20): 0.600 RSpredict(20): 0.402 Positive Predictive Value RNAalifold(20): 0.787 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	416 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.682 RSpredict(20): 0.533 Sensitivity MXScarna(seed): 0.601 RSpredict(20): 0.425 Positive Predictive Value MXScarna(seed): 0.774 RSpredict(20): 0.668 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.647 RSpredict(20): 0.487 Sensitivity MXScarna(20): 0.589 RSpredict(20): 0.402 Positive Predictive Value MXScarna(20): 0.710 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.609 RSpredict(20): 0.487 Sensitivity IPknot: 0.546 RSpredict(20): 0.402 Positive Predictive Value IPknot: 0.679 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.685 RSpredict(20): 0.514 Sensitivity Multilign(20): 0.617 RSpredict(20): 0.374 Positive Predictive Value Multilign(20): 0.762 RSpredict(20): 0.708 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.629 RSpredict(20): 0.552 Sensitivity Murlet(20): 0.503 RSpredict(20): 0.436 Positive Predictive Value Murlet(20): 0.787 RSpredict(20): 0.700 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.648 RSpredict(20): 0.513 Sensitivity RNAalifold(seed): 0.508 RSpredict(20): 0.412 Positive Predictive Value RNAalifold(seed): 0.826 RSpredict(20): 0.639 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	641 CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.569 RSpredict(20): 0.491 Sensitivity CentroidFold: 0.508 RSpredict(20): 0.405 Positive Predictive Value CentroidFold: 0.638 RSpredict(20): 0.595 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RSpredict(20) vs RNASampler(20) Matthews Correlation Coefficient RSpredict(20): 0.695 RNASampler(20): 0.676 Sensitivity RSpredict(20): 0.612 RNASampler(20): 0.522 Positive Predictive Value RSpredict(20): 0.790 RNASampler(20): 0.877 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.554 RSpredict(20): 0.487 Sensitivity Contrafold: 0.536 RSpredict(20): 0.402 Positive Predictive Value Contrafold: 0.572 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.530 RSpredict(20): 0.487 Sensitivity Sfold: 0.475 RSpredict(20): 0.402 Positive Predictive Value Sfold: 0.591 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 RSpredict(20) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(20): 0.739 Multilign(seed): 0.334 Sensitivity RSpredict(20): 0.698 Multilign(seed): 0.186 Positive Predictive Value RSpredict(20): 0.789 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	642 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.512 RSpredict(20): 0.487 Sensitivity MaxExpect: 0.499 RSpredict(20): 0.402 Positive Predictive Value MaxExpect: 0.527 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.507 RSpredict(20): 0.487 Sensitivity ProbKnot: 0.498 RSpredict(20): 0.402 Positive Predictive Value ProbKnot: 0.517 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RSpredict(20) vs Fold Matthews Correlation Coefficient RSpredict(20): 0.487 Fold: 0.485 Sensitivity RSpredict(20): 0.402 Fold: 0.486 Positive Predictive Value RSpredict(20): 0.590 Fold: 0.485 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 0.657358697881	42 RSpredict(20) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(20): 0.753 RNASampler(seed): 0.571 Sensitivity RSpredict(20): 0.684 RNASampler(seed): 0.343 Positive Predictive Value RSpredict(20): 0.833 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 5.23657817852e-08	642 UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.497 RSpredict(20): 0.487 Sensitivity UNAFold: 0.491 RSpredict(20): 0.402 Positive Predictive Value UNAFold: 0.503 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 1.97386617324e-07	565 RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.570 RSpredict(20): 0.524 Sensitivity RNAsubopt: 0.570 RSpredict(20): 0.385 Positive Predictive Value RNAsubopt: 0.573 RSpredict(20): 0.714 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CMfinder(20) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(20): 0.549 RSpredict(20): 0.525 Sensitivity CMfinder(20): 0.380 RSpredict(20): 0.387 Positive Predictive Value CMfinder(20): 0.794 RSpredict(20): 0.715 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs PknotsRG Matthews Correlation Coefficient RSpredict(20): 0.592 PknotsRG: 0.521 Sensitivity RSpredict(20): 0.477 PknotsRG: 0.514 Positive Predictive Value RSpredict(20): 0.736 PknotsRG: 0.529 Number of pairs reference - predicted secondary structure: 611 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.518 RSpredict(20): 0.487 Sensitivity Carnac(20): 0.301 RSpredict(20): 0.402 Positive Predictive Value Carnac(20): 0.892 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNAfold Matthews Correlation Coefficient RSpredict(20): 0.487 RNAfold: 0.482 Sensitivity RSpredict(20): 0.402 RNAfold: 0.480 Positive Predictive Value RSpredict(20): 0.590 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 4.28774587736e-06	= CMfinder(seed) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RSpredict(20): 0.729 Sensitivity CMfinder(seed): 0.607 RSpredict(20): 0.656 Positive Predictive Value CMfinder(seed): 0.898 RSpredict(20): 0.816 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.0179975597988	- Afold vs RSpredict(20) Matthews Correlation Coefficient Afold: 0.474 RSpredict(20): 0.460 Sensitivity Afold: 0.470 RSpredict(20): 0.378 Positive Predictive Value Afold: 0.479 RSpredict(20): 0.562 Number of pairs reference - predicted secondary structure: 421 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): 0.789 HotKnots: 0.698 Sensitivity RSpredict(20): 0.693 HotKnots: 0.695 Positive Predictive Value RSpredict(20): 0.901 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs CRWrnafold Matthews Correlation Coefficient RSpredict(20): 0.567 CRWrnafold: 0.541 Sensitivity RSpredict(20): 0.442 CRWrnafold: 0.532 Positive Predictive Value RSpredict(20): 0.727 CRWrnafold: 0.551 Number of pairs reference - predicted secondary structure: 590 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.821 Pknots: 0.655 Sensitivity RSpredict(20): 0.738 Pknots: 0.662 Positive Predictive Value RSpredict(20): 0.915 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.524 McQFold: 0.484 Sensitivity RSpredict(20): 0.385 McQFold: 0.464 Positive Predictive Value RSpredict(20): 0.714 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNAshapes Matthews Correlation Coefficient RSpredict(20): 0.533 RNAshapes: 0.526 Sensitivity RSpredict(20): 0.394 RNAshapes: 0.514 Positive Predictive Value RSpredict(20): 0.721 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.784 PPfold(seed): 0.453 Sensitivity RSpredict(20): 0.671 PPfold(seed): 0.224 Positive Predictive Value RSpredict(20): 0.917 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.387 Mastr(20): 0.296 Sensitivity RSpredict(20): 0.305 Mastr(20): 0.111 Positive Predictive Value RSpredict(20): 0.494 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(20): 0.748 Murlet(seed): 0.631 Sensitivity RSpredict(20): 0.667 Murlet(seed): 0.418 Positive Predictive Value RSpredict(20): 0.844 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RSpredict(20) vs RNASLOpt Matthews Correlation Coefficient RSpredict(20): 0.539 RNASLOpt: 0.500 Sensitivity RSpredict(20): 0.401 RNASLOpt: 0.464 Positive Predictive Value RSpredict(20): 0.725 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Cylofold Matthews Correlation Coefficient RSpredict(20): 0.794 Cylofold: 0.557 Sensitivity RSpredict(20): 0.700 Cylofold: 0.543 Positive Predictive Value RSpredict(20): 0.903 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.524 RNAwolf: 0.414 Sensitivity RSpredict(20): 0.385 RNAwolf: 0.423 Positive Predictive Value RSpredict(20): 0.714 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.529 Vsfold4: 0.390 Sensitivity RSpredict(20): 0.391 Vsfold4: 0.356 Positive Predictive Value RSpredict(20): 0.718 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.531 Vsfold5: 0.365 Sensitivity RSpredict(20): 0.393 Vsfold5: 0.341 Positive Predictive Value RSpredict(20): 0.719 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.821 Alterna: 0.618 Sensitivity RSpredict(20): 0.738 Alterna: 0.626 Positive Predictive Value RSpredict(20): 0.917 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.821 RDfolder: 0.556 Sensitivity RSpredict(20): 0.738 RDfolder: 0.511 Positive Predictive Value RSpredict(20): 0.917 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.744 Carnac(seed): 0.398 Sensitivity RSpredict(20): 0.655 Carnac(seed): 0.173 Positive Predictive Value RSpredict(20): 0.846 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.789 MCFold: 0.500 Sensitivity RSpredict(20): 0.690 MCFold: 0.559 Positive Predictive Value RSpredict(20): 0.905 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.524 RSpredict(seed): 0.410 Sensitivity RSpredict(20): 0.416 RSpredict(seed): 0.277 Positive Predictive Value RSpredict(20): 0.661 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.482 NanoFolder: 0.189 Sensitivity RSpredict(20): 0.342 NanoFolder: 0.218 Positive Predictive Value RSpredict(20): 0.682 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.453 Mastr(seed): 0.104 Sensitivity RSpredict(20): 0.313 Mastr(seed): 0.013 Positive Predictive Value RSpredict(20): 0.657 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(20)	19 TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 CMfinder(20): 0.650 Sensitivity TurboFold(seed): 0.851 CMfinder(20): 0.500 Positive Predictive Value TurboFold(seed): 0.867 CMfinder(20): 0.849 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	545 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.800 CMfinder(20): 0.554 Sensitivity PETfold_pre2.0(seed): 0.729 CMfinder(20): 0.387 Positive Predictive Value PETfold_pre2.0(seed): 0.878 CMfinder(20): 0.796 Number of pairs reference - predicted secondary structure: 545 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.863 CMfinder(20): 0.549 Sensitivity ContextFold: 0.823 CMfinder(20): 0.380 Positive Predictive Value ContextFold: 0.906 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.786 CMfinder(20): 0.549 Sensitivity TurboFold(20): 0.740 CMfinder(20): 0.380 Positive Predictive Value TurboFold(20): 0.837 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	340 CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.744 CMfinder(20): 0.519 Sensitivity CentroidAlifold(seed): 0.588 CMfinder(20): 0.350 Positive Predictive Value CentroidAlifold(seed): 0.943 CMfinder(20): 0.773 Number of pairs reference - predicted secondary structure: 340 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.767 CMfinder(20): 0.550 Sensitivity PETfold_pre2.0(20): 0.676 CMfinder(20): 0.381 Positive Predictive Value PETfold_pre2.0(20): 0.870 CMfinder(20): 0.795 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.758 CMfinder(20): 0.549 Sensitivity CentroidAlifold(20): 0.620 CMfinder(20): 0.380 Positive Predictive Value CentroidAlifold(20): 0.928 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 CMfinder(20): 0.549 Sensitivity CentroidHomfold‑LAST: 0.624 CMfinder(20): 0.380 Positive Predictive Value CentroidHomfold‑LAST: 0.899 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	549 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.760 CMfinder(20): 0.551 Sensitivity PPfold(20): 0.654 CMfinder(20): 0.382 Positive Predictive Value PPfold(20): 0.885 CMfinder(20): 0.795 Number of pairs reference - predicted secondary structure: 549 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.706 CMfinder(20): 0.549 Sensitivity RNAalifold(20): 0.578 CMfinder(20): 0.380 Positive Predictive Value RNAalifold(20): 0.863 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	354 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.701 CMfinder(20): 0.524 Sensitivity MXScarna(seed): 0.607 CMfinder(20): 0.354 Positive Predictive Value MXScarna(seed): 0.810 CMfinder(20): 0.777 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.702 CMfinder(20): 0.549 Sensitivity MXScarna(20): 0.636 CMfinder(20): 0.380 Positive Predictive Value MXScarna(20): 0.776 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.687 CMfinder(20): 0.549 Sensitivity IPknot: 0.628 CMfinder(20): 0.380 Positive Predictive Value IPknot: 0.752 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.686 CMfinder(20): 0.554 Sensitivity Multilign(20): 0.619 CMfinder(20): 0.385 Positive Predictive Value Multilign(20): 0.762 CMfinder(20): 0.799 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	491 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.631 CMfinder(20): 0.560 Sensitivity Murlet(20): 0.498 CMfinder(20): 0.394 Positive Predictive Value Murlet(20): 0.803 CMfinder(20): 0.797 Number of pairs reference - predicted secondary structure: 491 Wilcoxon single-rank test P-value: 3.56938820447e-08	336 CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.518 RNAalifold(seed): 0.508 Sensitivity CMfinder(20): 0.348 RNAalifold(seed): 0.303 Positive Predictive Value CMfinder(20): 0.772 RNAalifold(seed): 0.854 Number of pairs reference - predicted secondary structure: 336 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: 0.650 CMfinder(20): 0.549 Sensitivity CentroidFold: 0.594 CMfinder(20): 0.380 Positive Predictive Value CentroidFold: 0.712 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	389 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.677 CMfinder(20): 0.596 Sensitivity RNASampler(20): 0.524 CMfinder(20): 0.436 Positive Predictive Value RNASampler(20): 0.877 CMfinder(20): 0.815 Number of pairs reference - predicted secondary structure: 389 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.638 CMfinder(20): 0.549 Sensitivity Contrafold: 0.619 CMfinder(20): 0.380 Positive Predictive Value Contrafold: 0.658 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.613 CMfinder(20): 0.549 Sensitivity Sfold: 0.556 CMfinder(20): 0.380 Positive Predictive Value Sfold: 0.677 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 CMfinder(20) vs Multilign(seed) Matthews Correlation Coefficient CMfinder(20): 0.514 Multilign(seed): 0.334 Sensitivity CMfinder(20): 0.395 Multilign(seed): 0.186 Positive Predictive Value CMfinder(20): 0.680 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	561 MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.621 CMfinder(20): 0.549 Sensitivity MaxExpect: 0.601 CMfinder(20): 0.380 Positive Predictive Value MaxExpect: 0.644 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.619 CMfinder(20): 0.549 Sensitivity ProbKnot: 0.603 CMfinder(20): 0.380 Positive Predictive Value ProbKnot: 0.637 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.598 CMfinder(20): 0.549 Sensitivity Fold: 0.592 CMfinder(20): 0.380 Positive Predictive Value Fold: 0.606 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 CMfinder(20) vs RNASampler(seed) Matthews Correlation Coefficient CMfinder(20): 0.735 RNASampler(seed): 0.571 Sensitivity CMfinder(20): 0.607 RNASampler(seed): 0.343 Positive Predictive Value CMfinder(20): 0.894 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.586 CMfinder(20): 0.549 Sensitivity UNAFold: 0.574 CMfinder(20): 0.380 Positive Predictive Value UNAFold: 0.600 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.569 CMfinder(20): 0.549 Sensitivity RNAsubopt: 0.568 CMfinder(20): 0.380 Positive Predictive Value RNAsubopt: 0.572 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 CMfinder(20) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(20): 0.549 RSpredict(20): 0.525 Sensitivity CMfinder(20): 0.380 RSpredict(20): 0.387 Positive Predictive Value CMfinder(20): 0.794 RSpredict(20): 0.715 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08		- PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.565 CMfinder(20): 0.549 Sensitivity PknotsRG: 0.558 CMfinder(20): 0.380 Positive Predictive Value PknotsRG: 0.574 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Carnac(20) Matthews Correlation Coefficient CMfinder(20): 0.549 Carnac(20): 0.470 Sensitivity CMfinder(20): 0.380 Carnac(20): 0.249 Positive Predictive Value CMfinder(20): 0.794 Carnac(20): 0.889 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.578 CMfinder(20): 0.549 Sensitivity RNAfold: 0.571 CMfinder(20): 0.380 Positive Predictive Value RNAfold: 0.587 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 CMfinder(20): 0.711 Sensitivity CMfinder(seed): 0.607 CMfinder(20): 0.579 Positive Predictive Value CMfinder(seed): 0.898 CMfinder(20): 0.880 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.572 CMfinder(20): 0.534 Sensitivity Afold: 0.559 CMfinder(20): 0.365 Positive Predictive Value Afold: 0.586 CMfinder(20): 0.783 Number of pairs reference - predicted secondary structure: 346 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs HotKnots Matthews Correlation Coefficient CMfinder(20): 0.735 HotKnots: 0.696 Sensitivity CMfinder(20): 0.603 HotKnots: 0.693 Positive Predictive Value CMfinder(20): 0.899 HotKnots: 0.703 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs CRWrnafold Matthews Correlation Coefficient CMfinder(20): 0.549 CRWrnafold: 0.541 Sensitivity CMfinder(20): 0.380 CRWrnafold: 0.532 Positive Predictive Value CMfinder(20): 0.794 CRWrnafold: 0.552 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.791 Pknots: 0.655 Sensitivity CMfinder(20): 0.678 Pknots: 0.662 Positive Predictive Value CMfinder(20): 0.926 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.549 McQFold: 0.483 Sensitivity CMfinder(20): 0.380 McQFold: 0.463 Positive Predictive Value CMfinder(20): 0.794 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.557 RNAshapes: 0.525 Sensitivity CMfinder(20): 0.388 RNAshapes: 0.513 Positive Predictive Value CMfinder(20): 0.800 RNAshapes: 0.540 Number of pairs reference - predicted secondary structure: 551 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs PPfold(seed) Matthews Correlation Coefficient CMfinder(20): 0.711 PPfold(seed): 0.453 Sensitivity CMfinder(20): 0.563 PPfold(seed): 0.224 Positive Predictive Value CMfinder(20): 0.901 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.549 Mastr(20): 0.350 Sensitivity CMfinder(20): 0.380 Mastr(20): 0.155 Positive Predictive Value CMfinder(20): 0.794 Mastr(20): 0.789 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(20): 0.721 Murlet(seed): 0.631 Sensitivity CMfinder(20): 0.591 Murlet(seed): 0.418 Positive Predictive Value CMfinder(20): 0.884 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.560 RNASLOpt: 0.499 Sensitivity CMfinder(20): 0.392 RNASLOpt: 0.463 Positive Predictive Value CMfinder(20): 0.801 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Cylofold Matthews Correlation Coefficient CMfinder(20): 0.741 Cylofold: 0.559 Sensitivity CMfinder(20): 0.610 Cylofold: 0.546 Positive Predictive Value CMfinder(20): 0.903 Cylofold: 0.578 Number of pairs reference - predicted secondary structure: 300 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.549 RNAwolf: 0.414 Sensitivity CMfinder(20): 0.380 RNAwolf: 0.423 Positive Predictive Value CMfinder(20): 0.794 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.554 Vsfold4: 0.391 Sensitivity CMfinder(20): 0.385 Vsfold4: 0.357 Positive Predictive Value CMfinder(20): 0.798 Vsfold4: 0.432 Number of pairs reference - predicted secondary structure: 556 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.556 Vsfold5: 0.366 Sensitivity CMfinder(20): 0.388 Vsfold5: 0.342 Positive Predictive Value CMfinder(20): 0.799 Vsfold5: 0.395 Number of pairs reference - predicted secondary structure: 553 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Alterna Matthews Correlation Coefficient CMfinder(20): 0.792 Alterna: 0.618 Sensitivity CMfinder(20): 0.679 Alterna: 0.626 Positive Predictive Value CMfinder(20): 0.927 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.792 RDfolder: 0.556 Sensitivity CMfinder(20): 0.679 RDfolder: 0.511 Positive Predictive Value CMfinder(20): 0.927 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.599 Carnac(seed): 0.310 Sensitivity CMfinder(20): 0.453 Carnac(seed): 0.106 Positive Predictive Value CMfinder(20): 0.794 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.738 MCFold: 0.498 Sensitivity CMfinder(20): 0.608 MCFold: 0.558 Positive Predictive Value CMfinder(20): 0.898 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.520 RSpredict(seed): 0.239 Sensitivity CMfinder(20): 0.351 RSpredict(seed): 0.105 Positive Predictive Value CMfinder(20): 0.773 RSpredict(seed): 0.550 Number of pairs reference - predicted secondary structure: 342 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.525 NanoFolder: 0.187 Sensitivity CMfinder(20): 0.353 NanoFolder: 0.216 Positive Predictive Value CMfinder(20): 0.783 NanoFolder: 0.165 Number of pairs reference - predicted secondary structure: 114 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.526 Mastr(seed): 0.107 Sensitivity CMfinder(20): 0.358 Mastr(seed): 0.014 Positive Predictive Value CMfinder(20): 0.774 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 339 Wilcoxon single-rank test P-value: 3.56938820447e-08
PknotsRG	51 TurboFold(seed) vs PknotsRG Matthews Correlation Coefficient TurboFold(seed): 0.791 PknotsRG: 0.680 Sensitivity TurboFold(seed): 0.762 PknotsRG: 0.688 Positive Predictive Value TurboFold(seed): 0.822 PknotsRG: 0.674 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1193 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.756 PknotsRG: 0.507 Sensitivity PETfold_pre2.0(seed): 0.685 PknotsRG: 0.507 Positive Predictive Value PETfold_pre2.0(seed): 0.835 PknotsRG: 0.509 Number of pairs reference - predicted secondary structure: 1193 Wilcoxon single-rank test P-value: 3.56938820447e-08	1868 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.735 PknotsRG: 0.466 Sensitivity ContextFold: 0.697 PknotsRG: 0.467 Positive Predictive Value ContextFold: 0.776 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.787 PknotsRG: 0.566 Sensitivity TurboFold(20): 0.740 PknotsRG: 0.559 Positive Predictive Value TurboFold(20): 0.837 PknotsRG: 0.575 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	694 CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.762 PknotsRG: 0.529 Sensitivity CentroidAlifold(seed): 0.640 PknotsRG: 0.523 Positive Predictive Value CentroidAlifold(seed): 0.908 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 694 Wilcoxon single-rank test P-value: 3.56938820447e-08	608 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.792 PknotsRG: 0.521 Sensitivity PETfold_pre2.0(20): 0.728 PknotsRG: 0.514 Positive Predictive Value PETfold_pre2.0(20): 0.861 PknotsRG: 0.528 Number of pairs reference - predicted secondary structure: 608 Wilcoxon single-rank test P-value: 3.56938820447e-08	611 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.791 PknotsRG: 0.521 Sensitivity CentroidAlifold(20): 0.678 PknotsRG: 0.514 Positive Predictive Value CentroidAlifold(20): 0.923 PknotsRG: 0.529 Number of pairs reference - predicted secondary structure: 611 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 PknotsRG: 0.530 Sensitivity CentroidHomfold‑LAST: 0.527 PknotsRG: 0.530 Positive Predictive Value CentroidHomfold‑LAST: 0.850 PknotsRG: 0.531 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	556 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.763 PknotsRG: 0.559 Sensitivity PPfold(20): 0.658 PknotsRG: 0.551 Positive Predictive Value PPfold(20): 0.885 PknotsRG: 0.568 Number of pairs reference - predicted secondary structure: 556 Wilcoxon single-rank test P-value: 3.56938820447e-08	611 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.752 PknotsRG: 0.521 Sensitivity RNAalifold(20): 0.655 PknotsRG: 0.514 Positive Predictive Value RNAalifold(20): 0.864 PknotsRG: 0.529 Number of pairs reference - predicted secondary structure: 611 Wilcoxon single-rank test P-value: 3.56938820447e-08	716 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.668 PknotsRG: 0.529 Sensitivity MXScarna(seed): 0.579 PknotsRG: 0.524 Positive Predictive Value MXScarna(seed): 0.772 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 716 Wilcoxon single-rank test P-value: 3.56938820447e-08	611 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.699 PknotsRG: 0.521 Sensitivity MXScarna(20): 0.634 PknotsRG: 0.514 Positive Predictive Value MXScarna(20): 0.771 PknotsRG: 0.529 Number of pairs reference - predicted secondary structure: 611 Wilcoxon single-rank test P-value: 3.56938820447e-08	1868 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.587 PknotsRG: 0.466 Sensitivity IPknot: 0.525 PknotsRG: 0.467 Positive Predictive Value IPknot: 0.657 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.685 PknotsRG: 0.567 Sensitivity Multilign(20): 0.617 PknotsRG: 0.560 Positive Predictive Value Multilign(20): 0.762 PknotsRG: 0.576 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	501 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.644 PknotsRG: 0.556 Sensitivity Murlet(20): 0.514 PknotsRG: 0.551 Positive Predictive Value Murlet(20): 0.808 PknotsRG: 0.563 Number of pairs reference - predicted secondary structure: 501 Wilcoxon single-rank test P-value: 3.56938820447e-08	684 RNAalifold(seed) vs PknotsRG Matthews Correlation Coefficient RNAalifold(seed): 0.652 PknotsRG: 0.529 Sensitivity RNAalifold(seed): 0.490 PknotsRG: 0.523 Positive Predictive Value RNAalifold(seed): 0.869 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 684 Wilcoxon single-rank test P-value: 3.56938820447e-08	1868 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.553 PknotsRG: 0.466 Sensitivity CentroidFold: 0.494 PknotsRG: 0.467 Positive Predictive Value CentroidFold: 0.619 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.676 PknotsRG: 0.588 Sensitivity RNASampler(20): 0.522 PknotsRG: 0.589 Positive Predictive Value RNASampler(20): 0.877 PknotsRG: 0.589 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1868 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.541 PknotsRG: 0.466 Sensitivity Contrafold: 0.524 PknotsRG: 0.467 Positive Predictive Value Contrafold: 0.558 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	1868 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.508 PknotsRG: 0.466 Sensitivity Sfold: 0.459 PknotsRG: 0.467 Positive Predictive Value Sfold: 0.563 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs PknotsRG Matthews Correlation Coefficient Multilign(seed): 0.681 PknotsRG: 0.600 Sensitivity Multilign(seed): 0.649 PknotsRG: 0.615 Positive Predictive Value Multilign(seed): 0.717 PknotsRG: 0.586 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	1868 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.500 PknotsRG: 0.466 Sensitivity MaxExpect: 0.487 PknotsRG: 0.467 Positive Predictive Value MaxExpect: 0.514 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	1868 ProbKnot vs PknotsRG Matthews Correlation Coefficient ProbKnot: 0.496 PknotsRG: 0.466 Sensitivity ProbKnot: 0.492 PknotsRG: 0.467 Positive Predictive Value ProbKnot: 0.501 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	1868 Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.474 PknotsRG: 0.466 Sensitivity Fold: 0.478 PknotsRG: 0.467 Positive Predictive Value Fold: 0.472 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs PknotsRG Matthews Correlation Coefficient RNASampler(seed): 0.629 PknotsRG: 0.627 Sensitivity RNASampler(seed): 0.468 PknotsRG: 0.619 Positive Predictive Value RNASampler(seed): 0.847 PknotsRG: 0.637 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 0.657358697881	1868 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.474 PknotsRG: 0.466 Sensitivity UNAFold: 0.471 PknotsRG: 0.467 Positive Predictive Value UNAFold: 0.478 PknotsRG: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.530 RNAsubopt: 0.525 Sensitivity PknotsRG: 0.530 RNAsubopt: 0.530 Positive Predictive Value PknotsRG: 0.531 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	611 RSpredict(20) vs PknotsRG Matthews Correlation Coefficient RSpredict(20): 0.592 PknotsRG: 0.521 Sensitivity RSpredict(20): 0.477 PknotsRG: 0.514 Positive Predictive Value RSpredict(20): 0.736 PknotsRG: 0.529 Number of pairs reference - predicted secondary structure: 611 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.565 CMfinder(20): 0.549 Sensitivity PknotsRG: 0.558 CMfinder(20): 0.380 Positive Predictive Value PknotsRG: 0.574 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.534 PknotsRG: 0.521 Sensitivity Carnac(20): 0.315 PknotsRG: 0.514 Positive Predictive Value Carnac(20): 0.905 PknotsRG: 0.529 Number of pairs reference - predicted secondary structure: 611 Wilcoxon single-rank test P-value: 3.85233844192e-08	= PknotsRG vs RNAfold Matthews Correlation Coefficient PknotsRG: 0.466 RNAfold: 0.465 Sensitivity PknotsRG: 0.467 RNAfold: 0.467 Positive Predictive Value PknotsRG: 0.465 RNAfold: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 0.0929257687319	+ PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.604 CMfinder(seed): 0.486 Sensitivity PknotsRG: 0.604 CMfinder(seed): 0.312 Positive Predictive Value PknotsRG: 0.606 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Afold Matthews Correlation Coefficient PknotsRG: 0.467 Afold: 0.463 Sensitivity PknotsRG: 0.465 Afold: 0.460 Positive Predictive Value PknotsRG: 0.469 Afold: 0.467 Number of pairs reference - predicted secondary structure: 1199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs HotKnots Matthews Correlation Coefficient PknotsRG: 0.618 HotKnots: 0.613 Sensitivity PknotsRG: 0.610 HotKnots: 0.607 Positive Predictive Value PknotsRG: 0.630 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.469 CRWrnafold: 0.437 Sensitivity PknotsRG: 0.470 CRWrnafold: 0.440 Positive Predictive Value PknotsRG: 0.468 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs PknotsRG Matthews Correlation Coefficient Pknots: 0.606 PknotsRG: 0.603 Sensitivity Pknots: 0.595 PknotsRG: 0.595 Positive Predictive Value Pknots: 0.624 PknotsRG: 0.617 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 0.000349712763079	+ PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.520 McQFold: 0.467 Sensitivity PknotsRG: 0.522 McQFold: 0.457 Positive Predictive Value PknotsRG: 0.518 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.531 RNAshapes: 0.477 Sensitivity PknotsRG: 0.530 RNAshapes: 0.472 Positive Predictive Value PknotsRG: 0.533 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.678 PPfold(seed): 0.626 Sensitivity PknotsRG: 0.688 PPfold(seed): 0.495 Positive Predictive Value PknotsRG: 0.670 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.563 Mastr(20): 0.348 Sensitivity PknotsRG: 0.556 Mastr(20): 0.154 Positive Predictive Value PknotsRG: 0.571 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 566 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.598 Murlet(seed): 0.540 Sensitivity PknotsRG: 0.597 Murlet(seed): 0.360 Positive Predictive Value PknotsRG: 0.601 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.531 RNASLOpt: 0.470 Sensitivity PknotsRG: 0.531 RNASLOpt: 0.442 Positive Predictive Value PknotsRG: 0.533 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.637 Cylofold: 0.575 Sensitivity PknotsRG: 0.628 Cylofold: 0.551 Positive Predictive Value PknotsRG: 0.652 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.489 RNAwolf: 0.343 Sensitivity PknotsRG: 0.491 RNAwolf: 0.358 Positive Predictive Value PknotsRG: 0.488 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.529 Vsfold4: 0.346 Sensitivity PknotsRG: 0.529 Vsfold4: 0.318 Positive Predictive Value PknotsRG: 0.531 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.529 Vsfold5: 0.339 Sensitivity PknotsRG: 0.529 Vsfold5: 0.322 Positive Predictive Value PknotsRG: 0.531 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.605 Alterna: 0.552 Sensitivity PknotsRG: 0.598 Alterna: 0.547 Positive Predictive Value PknotsRG: 0.619 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.605 RDfolder: 0.520 Sensitivity PknotsRG: 0.598 RDfolder: 0.464 Positive Predictive Value PknotsRG: 0.619 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.589 Carnac(seed): 0.244 Sensitivity PknotsRG: 0.593 Carnac(seed): 0.069 Positive Predictive Value PknotsRG: 0.586 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.620 MCFold: 0.473 Sensitivity PknotsRG: 0.610 MCFold: 0.524 Positive Predictive Value PknotsRG: 0.635 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.534 RSpredict(seed): 0.395 Sensitivity PknotsRG: 0.529 RSpredict(seed): 0.238 Positive Predictive Value PknotsRG: 0.541 RSpredict(seed): 0.656 Number of pairs reference - predicted secondary structure: 690 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.542 NanoFolder: 0.194 Sensitivity PknotsRG: 0.540 NanoFolder: 0.229 Positive Predictive Value PknotsRG: 0.546 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.575 Mastr(seed): 0.114 Sensitivity PknotsRG: 0.571 Mastr(seed): 0.016 Positive Predictive Value PknotsRG: 0.580 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08
Carnac(20)	19 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 Carnac(20): 0.481 Sensitivity TurboFold(seed): 0.851 Carnac(20): 0.276 Positive Predictive Value TurboFold(seed): 0.867 Carnac(20): 0.840 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.79203144115e-08	626 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.778 Carnac(20): 0.522 Sensitivity PETfold_pre2.0(seed): 0.729 Carnac(20): 0.306 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.791 Carnac(20): 0.518 Sensitivity ContextFold: 0.752 Carnac(20): 0.301 Positive Predictive Value ContextFold: 0.832 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.787 Carnac(20): 0.469 Sensitivity TurboFold(20): 0.740 Carnac(20): 0.248 Positive Predictive Value TurboFold(20): 0.837 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 Carnac(20): 0.506 Sensitivity CentroidAlifold(seed): 0.652 Carnac(20): 0.283 Positive Predictive Value CentroidAlifold(seed): 0.918 Carnac(20): 0.903 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 Carnac(20): 0.519 Sensitivity PETfold_pre2.0(20): 0.686 Carnac(20): 0.302 Positive Predictive Value PETfold_pre2.0(20): 0.807 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.740 Carnac(20): 0.518 Sensitivity CentroidAlifold(20): 0.616 Carnac(20): 0.301 Positive Predictive Value CentroidAlifold(20): 0.891 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 Carnac(20): 0.469 Sensitivity CentroidHomfold‑LAST: 0.625 Carnac(20): 0.248 Positive Predictive Value CentroidHomfold‑LAST: 0.899 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.758 Carnac(20): 0.482 Sensitivity PPfold(20): 0.654 Carnac(20): 0.260 Positive Predictive Value PPfold(20): 0.879 Carnac(20): 0.896 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.687 Carnac(20): 0.518 Sensitivity RNAalifold(20): 0.600 Carnac(20): 0.301 Positive Predictive Value RNAalifold(20): 0.787 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	416 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.682 Carnac(20): 0.508 Sensitivity MXScarna(seed): 0.601 Carnac(20): 0.285 Positive Predictive Value MXScarna(seed): 0.774 Carnac(20): 0.903 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.647 Carnac(20): 0.518 Sensitivity MXScarna(20): 0.589 Carnac(20): 0.301 Positive Predictive Value MXScarna(20): 0.710 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.609 Carnac(20): 0.518 Sensitivity IPknot: 0.546 Carnac(20): 0.301 Positive Predictive Value IPknot: 0.679 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.685 Carnac(20): 0.467 Sensitivity Multilign(20): 0.617 Carnac(20): 0.245 Positive Predictive Value Multilign(20): 0.762 Carnac(20): 0.891 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.629 Carnac(20): 0.512 Sensitivity Murlet(20): 0.503 Carnac(20): 0.296 Positive Predictive Value Murlet(20): 0.787 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.648 Carnac(20): 0.502 Sensitivity RNAalifold(seed): 0.508 Carnac(20): 0.280 Positive Predictive Value RNAalifold(seed): 0.826 Carnac(20): 0.902 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	641 CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.569 Carnac(20): 0.518 Sensitivity CentroidFold: 0.508 Carnac(20): 0.301 Positive Predictive Value CentroidFold: 0.638 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.676 Carnac(20): 0.586 Sensitivity RNASampler(20): 0.522 Carnac(20): 0.385 Positive Predictive Value RNASampler(20): 0.877 Carnac(20): 0.894 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.554 Carnac(20): 0.518 Sensitivity Contrafold: 0.536 Carnac(20): 0.301 Positive Predictive Value Contrafold: 0.572 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.530 Carnac(20): 0.518 Sensitivity Sfold: 0.475 Carnac(20): 0.301 Positive Predictive Value Sfold: 0.591 Carnac(20): 0.892 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 Carnac(20) vs Multilign(seed) Matthews Correlation Coefficient Carnac(20): 0.588 Multilign(seed): 0.334 Sensitivity Carnac(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value Carnac(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	642 Carnac(20) vs MaxExpect Matthews Correlation Coefficient Carnac(20): 0.518 MaxExpect: 0.512 Sensitivity Carnac(20): 0.301 MaxExpect: 0.499 Positive Predictive Value Carnac(20): 0.892 MaxExpect: 0.527 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 8.1815824276e-08	642 Carnac(20) vs ProbKnot Matthews Correlation Coefficient Carnac(20): 0.518 ProbKnot: 0.507 Sensitivity Carnac(20): 0.301 ProbKnot: 0.498 Positive Predictive Value Carnac(20): 0.892 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 Carnac(20) vs Fold Matthews Correlation Coefficient Carnac(20): 0.518 Fold: 0.485 Sensitivity Carnac(20): 0.301 Fold: 0.486 Positive Predictive Value Carnac(20): 0.892 Fold: 0.485 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.571 Carnac(20): 0.461 Sensitivity RNASampler(seed): 0.343 Carnac(20): 0.241 Positive Predictive Value RNASampler(seed): 0.957 Carnac(20): 0.893 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.518 UNAFold: 0.497 Sensitivity Carnac(20): 0.301 UNAFold: 0.491 Positive Predictive Value Carnac(20): 0.892 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 RNAsubopt vs Carnac(20) Matthews Correlation Coefficient RNAsubopt: 0.570 Carnac(20): 0.469 Sensitivity RNAsubopt: 0.570 Carnac(20): 0.248 Positive Predictive Value RNAsubopt: 0.573 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.518 RSpredict(20): 0.487 Sensitivity Carnac(20): 0.301 RSpredict(20): 0.402 Positive Predictive Value Carnac(20): 0.892 RSpredict(20): 0.590 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 CMfinder(20) vs Carnac(20) Matthews Correlation Coefficient CMfinder(20): 0.549 Carnac(20): 0.470 Sensitivity CMfinder(20): 0.380 Carnac(20): 0.249 Positive Predictive Value CMfinder(20): 0.794 Carnac(20): 0.889 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	611 Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.534 PknotsRG: 0.521 Sensitivity Carnac(20): 0.315 PknotsRG: 0.514 Positive Predictive Value Carnac(20): 0.905 PknotsRG: 0.529 Number of pairs reference - predicted secondary structure: 611 Wilcoxon single-rank test P-value: 3.85233844192e-08		+ Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.518 RNAfold: 0.482 Sensitivity Carnac(20): 0.301 RNAfold: 0.480 Positive Predictive Value Carnac(20): 0.892 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Carnac(20): 0.413 Sensitivity CMfinder(seed): 0.607 Carnac(20): 0.190 Positive Predictive Value CMfinder(seed): 0.898 Carnac(20): 0.911 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.501 Afold: 0.474 Sensitivity Carnac(20): 0.281 Afold: 0.470 Positive Predictive Value Carnac(20): 0.893 Afold: 0.479 Number of pairs reference - predicted secondary structure: 421 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs Carnac(20) Matthews Correlation Coefficient HotKnots: 0.698 Carnac(20): 0.675 Sensitivity HotKnots: 0.695 Carnac(20): 0.500 Positive Predictive Value HotKnots: 0.705 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.541 Carnac(20): 0.510 Sensitivity CRWrnafold: 0.532 Carnac(20): 0.289 Positive Predictive Value CRWrnafold: 0.551 Carnac(20): 0.900 Number of pairs reference - predicted secondary structure: 590 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.742 Pknots: 0.655 Sensitivity Carnac(20): 0.588 Pknots: 0.662 Positive Predictive Value Carnac(20): 0.940 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	- McQFold vs Carnac(20) Matthews Correlation Coefficient McQFold: 0.484 Carnac(20): 0.469 Sensitivity McQFold: 0.464 Carnac(20): 0.248 Positive Predictive Value McQFold: 0.507 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.526 Carnac(20): 0.472 Sensitivity RNAshapes: 0.514 Carnac(20): 0.251 Positive Predictive Value RNAshapes: 0.541 Carnac(20): 0.890 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.487 PPfold(seed): 0.453 Sensitivity Carnac(20): 0.277 PPfold(seed): 0.224 Positive Predictive Value Carnac(20): 0.861 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 6.32937386918e-08	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.462 Mastr(20): 0.296 Sensitivity Carnac(20): 0.246 Mastr(20): 0.111 Positive Predictive Value Carnac(20): 0.869 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs Carnac(20) Matthews Correlation Coefficient Murlet(seed): 0.631 Carnac(20): 0.444 Sensitivity Murlet(seed): 0.418 Carnac(20): 0.223 Positive Predictive Value Murlet(seed): 0.956 Carnac(20): 0.890 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 5.23657817852e-08	- RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.500 Carnac(20): 0.473 Sensitivity RNASLOpt: 0.464 Carnac(20): 0.252 Positive Predictive Value RNASLOpt: 0.542 Carnac(20): 0.889 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Cylofold Matthews Correlation Coefficient Carnac(20): 0.676 Cylofold: 0.557 Sensitivity Carnac(20): 0.499 Cylofold: 0.543 Positive Predictive Value Carnac(20): 0.918 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.469 RNAwolf: 0.414 Sensitivity Carnac(20): 0.248 RNAwolf: 0.423 Positive Predictive Value Carnac(20): 0.888 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.470 Vsfold4: 0.390 Sensitivity Carnac(20): 0.249 Vsfold4: 0.356 Positive Predictive Value Carnac(20): 0.889 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.472 Vsfold5: 0.365 Sensitivity Carnac(20): 0.251 Vsfold5: 0.341 Positive Predictive Value Carnac(20): 0.889 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.744 Alterna: 0.618 Sensitivity Carnac(20): 0.591 Alterna: 0.626 Positive Predictive Value Carnac(20): 0.940 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.744 RDfolder: 0.556 Sensitivity Carnac(20): 0.591 RDfolder: 0.511 Positive Predictive Value Carnac(20): 0.940 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.531 Carnac(seed): 0.398 Sensitivity Carnac(20): 0.310 Carnac(seed): 0.173 Positive Predictive Value Carnac(20): 0.913 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.677 MCFold: 0.500 Sensitivity Carnac(20): 0.505 MCFold: 0.559 Positive Predictive Value Carnac(20): 0.912 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.501 RSpredict(seed): 0.410 Sensitivity Carnac(20): 0.278 RSpredict(seed): 0.277 Positive Predictive Value Carnac(20): 0.904 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.464 NanoFolder: 0.189 Sensitivity Carnac(20): 0.244 NanoFolder: 0.218 Positive Predictive Value Carnac(20): 0.884 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.398 Mastr(seed): 0.104 Sensitivity Carnac(20): 0.180 Mastr(seed): 0.013 Positive Predictive Value Carnac(20): 0.881 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAfold	51 TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.791 RNAfold: 0.688 Sensitivity TurboFold(seed): 0.762 RNAfold: 0.693 Positive Predictive Value TurboFold(seed): 0.822 RNAfold: 0.685 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1224 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 RNAfold: 0.483 Sensitivity PETfold_pre2.0(seed): 0.675 RNAfold: 0.484 Positive Predictive Value PETfold_pre2.0(seed): 0.814 RNAfold: 0.483 Number of pairs reference - predicted secondary structure: 1224 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.686 RNAfold: 0.440 Sensitivity ContextFold: 0.648 RNAfold: 0.443 Positive Predictive Value ContextFold: 0.725 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.787 RNAfold: 0.579 Sensitivity TurboFold(20): 0.740 RNAfold: 0.572 Positive Predictive Value TurboFold(20): 0.837 RNAfold: 0.588 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.749 RNAfold: 0.520 Sensitivity CentroidAlifold(seed): 0.623 RNAfold: 0.515 Positive Predictive Value CentroidAlifold(seed): 0.901 RNAfold: 0.526 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	639 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.744 RNAfold: 0.481 Sensitivity PETfold_pre2.0(20): 0.686 RNAfold: 0.480 Positive Predictive Value PETfold_pre2.0(20): 0.807 RNAfold: 0.483 Number of pairs reference - predicted secondary structure: 639 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 RNAfold: 0.482 Sensitivity CentroidAlifold(20): 0.616 RNAfold: 0.480 Positive Predictive Value CentroidAlifold(20): 0.891 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 RNAfold: 0.531 Sensitivity CentroidHomfold‑LAST: 0.527 RNAfold: 0.531 Positive Predictive Value CentroidHomfold‑LAST: 0.850 RNAfold: 0.533 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	558 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.758 RNAfold: 0.566 Sensitivity PPfold(20): 0.654 RNAfold: 0.559 Positive Predictive Value PPfold(20): 0.879 RNAfold: 0.575 Number of pairs reference - predicted secondary structure: 558 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.687 RNAfold: 0.482 Sensitivity RNAalifold(20): 0.600 RNAfold: 0.480 Positive Predictive Value RNAalifold(20): 0.787 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	728 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.654 RNAfold: 0.521 Sensitivity MXScarna(seed): 0.568 RNAfold: 0.516 Positive Predictive Value MXScarna(seed): 0.753 RNAfold: 0.526 Number of pairs reference - predicted secondary structure: 728 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.647 RNAfold: 0.482 Sensitivity MXScarna(20): 0.589 RNAfold: 0.480 Positive Predictive Value MXScarna(20): 0.710 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	1972 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.563 RNAfold: 0.441 Sensitivity IPknot: 0.501 RNAfold: 0.444 Positive Predictive Value IPknot: 0.632 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 1972 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.685 RNAfold: 0.580 Sensitivity Multilign(20): 0.617 RNAfold: 0.573 Positive Predictive Value Multilign(20): 0.762 RNAfold: 0.589 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.629 RNAfold: 0.553 Sensitivity Murlet(20): 0.503 RNAfold: 0.548 Positive Predictive Value Murlet(20): 0.787 RNAfold: 0.559 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	700 RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.634 RNAfold: 0.515 Sensitivity RNAalifold(seed): 0.482 RNAfold: 0.511 Positive Predictive Value RNAalifold(seed): 0.835 RNAfold: 0.520 Number of pairs reference - predicted secondary structure: 700 Wilcoxon single-rank test P-value: 3.56938820447e-08	1915 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.534 RNAfold: 0.446 Sensitivity CentroidFold: 0.475 RNAfold: 0.449 Positive Predictive Value CentroidFold: 0.600 RNAfold: 0.443 Number of pairs reference - predicted secondary structure: 1915 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.676 RNAfold: 0.594 Sensitivity RNASampler(20): 0.522 RNAfold: 0.595 Positive Predictive Value RNASampler(20): 0.877 RNAfold: 0.596 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.521 RNAfold: 0.440 Sensitivity Contrafold: 0.506 RNAfold: 0.443 Positive Predictive Value Contrafold: 0.537 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.481 RNAfold: 0.440 Sensitivity Sfold: 0.433 RNAfold: 0.443 Positive Predictive Value Sfold: 0.535 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.681 RNAfold: 0.593 Sensitivity Multilign(seed): 0.649 RNAfold: 0.604 Positive Predictive Value Multilign(seed): 0.717 RNAfold: 0.585 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	1973 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.476 RNAfold: 0.440 Sensitivity MaxExpect: 0.465 RNAfold: 0.443 Positive Predictive Value MaxExpect: 0.488 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.471 RNAfold: 0.440 Sensitivity ProbKnot: 0.468 RNAfold: 0.443 Positive Predictive Value ProbKnot: 0.475 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1973 Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.448 RNAfold: 0.440 Sensitivity Fold: 0.453 RNAfold: 0.443 Positive Predictive Value Fold: 0.444 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): 0.629 RNAfold: 0.609 Sensitivity RNASampler(seed): 0.468 RNAfold: 0.594 Positive Predictive Value RNASampler(seed): 0.847 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.85233844192e-08	1973 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.447 RNAfold: 0.440 Sensitivity UNAFold: 0.446 RNAfold: 0.443 Positive Predictive Value UNAFold: 0.448 RNAfold: 0.437 Number of pairs reference - predicted secondary structure: 1973 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.531 RNAsubopt: 0.525 Sensitivity RNAfold: 0.531 RNAsubopt: 0.530 Positive Predictive Value RNAfold: 0.533 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 RSpredict(20) vs RNAfold Matthews Correlation Coefficient RSpredict(20): 0.487 RNAfold: 0.482 Sensitivity RSpredict(20): 0.402 RNAfold: 0.480 Positive Predictive Value RSpredict(20): 0.590 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 4.28774587736e-06	561 RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.578 CMfinder(20): 0.549 Sensitivity RNAfold: 0.571 CMfinder(20): 0.380 Positive Predictive Value RNAfold: 0.587 CMfinder(20): 0.794 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	1868 PknotsRG vs RNAfold Matthews Correlation Coefficient PknotsRG: 0.466 RNAfold: 0.465 Sensitivity PknotsRG: 0.467 RNAfold: 0.467 Positive Predictive Value PknotsRG: 0.465 RNAfold: 0.465 Number of pairs reference - predicted secondary structure: 1868 Wilcoxon single-rank test P-value: 0.0929257687319	642 Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.518 RNAfold: 0.482 Sensitivity Carnac(20): 0.301 RNAfold: 0.480 Positive Predictive Value Carnac(20): 0.892 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAfold vs CMfinder(seed) Matthews Correlation Coefficient RNAfold: 0.592 CMfinder(seed): 0.486 Sensitivity RNAfold: 0.589 CMfinder(seed): 0.312 Positive Predictive Value RNAfold: 0.597 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Afold Matthews Correlation Coefficient RNAfold: 0.436 Afold: 0.434 Sensitivity RNAfold: 0.437 Afold: 0.433 Positive Predictive Value RNAfold: 0.435 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	= HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.613 RNAfold: 0.612 Sensitivity HotKnots: 0.607 RNAfold: 0.604 Positive Predictive Value HotKnots: 0.624 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 0.041044797429	+ RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.468 CRWrnafold: 0.437 Sensitivity RNAfold: 0.470 CRWrnafold: 0.440 Positive Predictive Value RNAfold: 0.468 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs RNAfold Matthews Correlation Coefficient Pknots: 0.606 RNAfold: 0.596 Sensitivity Pknots: 0.595 RNAfold: 0.588 Positive Predictive Value Pknots: 0.624 RNAfold: 0.611 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.518 McQFold: 0.467 Sensitivity RNAfold: 0.521 McQFold: 0.457 Positive Predictive Value RNAfold: 0.517 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.533 RNAshapes: 0.477 Sensitivity RNAfold: 0.532 RNAshapes: 0.472 Positive Predictive Value RNAfold: 0.535 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.678 PPfold(seed): 0.626 Sensitivity RNAfold: 0.685 PPfold(seed): 0.495 Positive Predictive Value RNAfold: 0.672 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.497 Mastr(20): 0.296 Sensitivity RNAfold: 0.497 Mastr(20): 0.111 Positive Predictive Value RNAfold: 0.498 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.596 Murlet(seed): 0.540 Sensitivity RNAfold: 0.590 Murlet(seed): 0.360 Positive Predictive Value RNAfold: 0.603 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.534 RNASLOpt: 0.470 Sensitivity RNAfold: 0.534 RNASLOpt: 0.442 Positive Predictive Value RNAfold: 0.537 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.635 Cylofold: 0.575 Sensitivity RNAfold: 0.624 Cylofold: 0.551 Positive Predictive Value RNAfold: 0.651 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.487 RNAwolf: 0.343 Sensitivity RNAfold: 0.489 RNAwolf: 0.358 Positive Predictive Value RNAfold: 0.487 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.531 Vsfold4: 0.346 Sensitivity RNAfold: 0.531 Vsfold4: 0.318 Positive Predictive Value RNAfold: 0.533 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.531 Vsfold5: 0.339 Sensitivity RNAfold: 0.530 Vsfold5: 0.322 Positive Predictive Value RNAfold: 0.533 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.596 Alterna: 0.552 Sensitivity RNAfold: 0.589 Alterna: 0.547 Positive Predictive Value RNAfold: 0.611 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.596 RDfolder: 0.520 Sensitivity RNAfold: 0.589 RDfolder: 0.464 Positive Predictive Value RNAfold: 0.611 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.586 Carnac(seed): 0.244 Sensitivity RNAfold: 0.588 Carnac(seed): 0.069 Positive Predictive Value RNAfold: 0.585 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.615 MCFold: 0.473 Sensitivity RNAfold: 0.604 MCFold: 0.524 Positive Predictive Value RNAfold: 0.632 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.524 RSpredict(seed): 0.369 Sensitivity RNAfold: 0.519 RSpredict(seed): 0.229 Positive Predictive Value RNAfold: 0.529 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.550 NanoFolder: 0.194 Sensitivity RNAfold: 0.547 NanoFolder: 0.229 Positive Predictive Value RNAfold: 0.555 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.577 Mastr(seed): 0.113 Sensitivity RNAfold: 0.572 Mastr(seed): 0.016 Positive Predictive Value RNAfold: 0.583 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(seed)	24 TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): 0.817 CMfinder(seed): 0.576 Sensitivity TurboFold(seed): 0.766 CMfinder(seed): 0.440 Positive Predictive Value TurboFold(seed): 0.873 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	129 PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.764 CMfinder(seed): 0.486 Sensitivity PETfold_pre2.0(seed): 0.661 CMfinder(seed): 0.312 Positive Predictive Value PETfold_pre2.0(seed): 0.882 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.774 CMfinder(seed): 0.486 Sensitivity ContextFold: 0.739 CMfinder(seed): 0.312 Positive Predictive Value ContextFold: 0.812 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): 0.744 CMfinder(seed): 0.736 Sensitivity TurboFold(20): 0.678 CMfinder(seed): 0.607 Positive Predictive Value TurboFold(20): 0.821 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 1.15003019969e-05	129 CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.766 CMfinder(seed): 0.486 Sensitivity CentroidAlifold(seed): 0.635 CMfinder(seed): 0.312 Positive Predictive Value CentroidAlifold(seed): 0.925 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 PETfold_pre2.0(20): 0.708 Sensitivity CMfinder(seed): 0.607 PETfold_pre2.0(20): 0.594 Positive Predictive Value CMfinder(seed): 0.898 PETfold_pre2.0(20): 0.851 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 CentroidAlifold(20) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.805 CMfinder(seed): 0.736 Sensitivity CentroidAlifold(20): 0.718 CMfinder(seed): 0.607 Positive Predictive Value CentroidAlifold(20): 0.907 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	129 CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.725 CMfinder(seed): 0.486 Sensitivity CentroidHomfold‑LAST: 0.598 CMfinder(seed): 0.312 Positive Predictive Value CentroidHomfold‑LAST: 0.880 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs PPfold(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 PPfold(20): 0.656 Sensitivity CMfinder(seed): 0.607 PPfold(20): 0.507 Positive Predictive Value CMfinder(seed): 0.898 PPfold(20): 0.856 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs RNAalifold(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RNAalifold(20): 0.620 Sensitivity CMfinder(seed): 0.607 RNAalifold(20): 0.466 Positive Predictive Value CMfinder(seed): 0.898 RNAalifold(20): 0.832 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 MXScarna(seed) vs CMfinder(seed) Matthews Correlation Coefficient MXScarna(seed): 0.697 CMfinder(seed): 0.486 Sensitivity MXScarna(seed): 0.619 CMfinder(seed): 0.312 Positive Predictive Value MXScarna(seed): 0.785 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 MXScarna(20) vs CMfinder(seed) Matthews Correlation Coefficient MXScarna(20): 0.820 CMfinder(seed): 0.736 Sensitivity MXScarna(20): 0.785 CMfinder(seed): 0.607 Positive Predictive Value MXScarna(20): 0.860 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.700 CMfinder(seed): 0.486 Sensitivity IPknot: 0.661 CMfinder(seed): 0.312 Positive Predictive Value IPknot: 0.742 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Multilign(20): 0.657 Sensitivity CMfinder(seed): 0.607 Multilign(20): 0.508 Positive Predictive Value CMfinder(seed): 0.898 Multilign(20): 0.856 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 CMfinder(seed) vs Murlet(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Murlet(20): 0.649 Sensitivity CMfinder(seed): 0.607 Murlet(20): 0.483 Positive Predictive Value CMfinder(seed): 0.898 Murlet(20): 0.878 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	129 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.693 CMfinder(seed): 0.486 Sensitivity RNAalifold(seed): 0.532 CMfinder(seed): 0.312 Positive Predictive Value RNAalifold(seed): 0.904 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.671 CMfinder(seed): 0.486 Sensitivity CentroidFold: 0.617 CMfinder(seed): 0.312 Positive Predictive Value CentroidFold: 0.730 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs RNASampler(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RNASampler(20): 0.593 Sensitivity CMfinder(seed): 0.607 RNASampler(20): 0.399 Positive Predictive Value CMfinder(seed): 0.898 RNASampler(20): 0.888 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	129 Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.658 CMfinder(seed): 0.486 Sensitivity Contrafold: 0.642 CMfinder(seed): 0.312 Positive Predictive Value Contrafold: 0.676 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 Sfold vs CMfinder(seed) Matthews Correlation Coefficient Sfold: 0.645 CMfinder(seed): 0.486 Sensitivity Sfold: 0.594 CMfinder(seed): 0.312 Positive Predictive Value Sfold: 0.703 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): 0.767 CMfinder(seed): 0.531 Sensitivity Multilign(seed): 0.697 CMfinder(seed): 0.393 Positive Predictive Value Multilign(seed): 0.845 CMfinder(seed): 0.719 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.61939086268e-08	129 MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.594 CMfinder(seed): 0.486 Sensitivity MaxExpect: 0.583 CMfinder(seed): 0.312 Positive Predictive Value MaxExpect: 0.608 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: 0.592 CMfinder(seed): 0.486 Sensitivity ProbKnot: 0.584 CMfinder(seed): 0.312 Positive Predictive Value ProbKnot: 0.601 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.590 CMfinder(seed): 0.486 Sensitivity Fold: 0.591 CMfinder(seed): 0.312 Positive Predictive Value Fold: 0.590 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	90 RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): 0.631 CMfinder(seed): 0.560 Sensitivity RNASampler(seed): 0.472 CMfinder(seed): 0.424 Positive Predictive Value RNASampler(seed): 0.845 CMfinder(seed): 0.743 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.610 CMfinder(seed): 0.486 Sensitivity UNAFold: 0.602 CMfinder(seed): 0.312 Positive Predictive Value UNAFold: 0.620 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 RNAsubopt vs CMfinder(seed) Matthews Correlation Coefficient RNAsubopt: 0.585 CMfinder(seed): 0.486 Sensitivity RNAsubopt: 0.587 CMfinder(seed): 0.312 Positive Predictive Value RNAsubopt: 0.584 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RSpredict(20): 0.729 Sensitivity CMfinder(seed): 0.607 RSpredict(20): 0.656 Positive Predictive Value CMfinder(seed): 0.898 RSpredict(20): 0.816 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.0179975597988	38 CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 CMfinder(20): 0.711 Sensitivity CMfinder(seed): 0.607 CMfinder(20): 0.579 Positive Predictive Value CMfinder(seed): 0.898 CMfinder(20): 0.880 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.604 CMfinder(seed): 0.486 Sensitivity PknotsRG: 0.604 CMfinder(seed): 0.312 Positive Predictive Value PknotsRG: 0.606 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Carnac(20): 0.413 Sensitivity CMfinder(seed): 0.607 Carnac(20): 0.190 Positive Predictive Value CMfinder(seed): 0.898 Carnac(20): 0.911 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.1503931209e-08	129 RNAfold vs CMfinder(seed) Matthews Correlation Coefficient RNAfold: 0.592 CMfinder(seed): 0.486 Sensitivity RNAfold: 0.589 CMfinder(seed): 0.312 Positive Predictive Value RNAfold: 0.597 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Afold vs CMfinder(seed) Matthews Correlation Coefficient Afold: 0.616 CMfinder(seed): 0.489 Sensitivity Afold: 0.610 CMfinder(seed): 0.317 Positive Predictive Value Afold: 0.624 CMfinder(seed): 0.755 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs HotKnots Matthews Correlation Coefficient CMfinder(seed): 0.582 HotKnots: 0.503 Sensitivity CMfinder(seed): 0.446 HotKnots: 0.492 Positive Predictive Value CMfinder(seed): 0.765 HotKnots: 0.521 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: 0.556 CMfinder(seed): 0.486 Sensitivity CRWrnafold: 0.554 CMfinder(seed): 0.312 Positive Predictive Value CRWrnafold: 0.559 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Pknots Matthews Correlation Coefficient CMfinder(seed): 0.512 Pknots: 0.398 Sensitivity CMfinder(seed): 0.382 Pknots: 0.381 Positive Predictive Value CMfinder(seed): 0.696 Pknots: 0.429 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	- McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: 0.502 CMfinder(seed): 0.486 Sensitivity McQFold: 0.485 CMfinder(seed): 0.312 Positive Predictive Value McQFold: 0.520 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 1.70738736246e-07	- RNAshapes vs CMfinder(seed) Matthews Correlation Coefficient RNAshapes: 0.555 CMfinder(seed): 0.489 Sensitivity RNAshapes: 0.548 CMfinder(seed): 0.316 Positive Predictive Value RNAshapes: 0.564 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): 0.861 CMfinder(seed): 0.566 Sensitivity PPfold(seed): 0.774 CMfinder(seed): 0.427 Positive Predictive Value PPfold(seed): 0.959 CMfinder(seed): 0.752 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.98172311752e-08	- Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): 0.748 CMfinder(seed): 0.736 Sensitivity Mastr(20): 0.683 CMfinder(seed): 0.607 Positive Predictive Value Mastr(20): 0.824 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 1.47584956762e-07	- Murlet(seed) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(seed): 0.555 CMfinder(seed): 0.531 Sensitivity Murlet(seed): 0.351 CMfinder(seed): 0.382 Positive Predictive Value Murlet(seed): 0.879 CMfinder(seed): 0.741 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): 0.495 RNASLOpt: 0.489 Sensitivity CMfinder(seed): 0.325 RNASLOpt: 0.458 Positive Predictive Value CMfinder(seed): 0.755 RNASLOpt: 0.524 Number of pairs reference - predicted secondary structure: 125 Wilcoxon single-rank test P-value: 0.00297289556633	+ CMfinder(seed) vs Cylofold Matthews Correlation Coefficient CMfinder(seed): 0.599 Cylofold: 0.465 Sensitivity CMfinder(seed): 0.469 Cylofold: 0.415 Positive Predictive Value CMfinder(seed): 0.772 Cylofold: 0.531 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.486 RNAwolf: 0.414 Sensitivity CMfinder(seed): 0.312 RNAwolf: 0.424 Positive Predictive Value CMfinder(seed): 0.757 RNAwolf: 0.406 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Vsfold4 Matthews Correlation Coefficient CMfinder(seed): 0.488 Vsfold4: 0.303 Sensitivity CMfinder(seed): 0.316 Vsfold4: 0.277 Positive Predictive Value CMfinder(seed): 0.755 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Vsfold5 Matthews Correlation Coefficient CMfinder(seed): 0.488 Vsfold5: 0.285 Sensitivity CMfinder(seed): 0.316 Vsfold5: 0.272 Positive Predictive Value CMfinder(seed): 0.755 Vsfold5: 0.301 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): 0.512 Alterna: 0.405 Sensitivity CMfinder(seed): 0.382 Alterna: 0.380 Positive Predictive Value CMfinder(seed): 0.696 Alterna: 0.445 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs RDfolder Matthews Correlation Coefficient CMfinder(seed): 0.512 RDfolder: 0.317 Sensitivity CMfinder(seed): 0.382 RDfolder: 0.254 Positive Predictive Value CMfinder(seed): 0.696 RDfolder: 0.411 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): 0.486 Carnac(seed): 0.306 Sensitivity CMfinder(seed): 0.314 Carnac(seed): 0.110 Positive Predictive Value CMfinder(seed): 0.755 Carnac(seed): 0.857 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): 0.555 MCFold: 0.396 Sensitivity CMfinder(seed): 0.421 MCFold: 0.436 Positive Predictive Value CMfinder(seed): 0.736 MCFold: 0.367 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CMfinder(seed) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(seed): 0.486 RSpredict(seed): 0.484 Sensitivity CMfinder(seed): 0.312 RSpredict(seed): 0.331 Positive Predictive Value CMfinder(seed): 0.757 RSpredict(seed): 0.709 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 0.375011270663	+ CMfinder(seed) vs NanoFolder Matthews Correlation Coefficient CMfinder(seed): 0.454 NanoFolder: 0.216 Sensitivity CMfinder(seed): 0.267 NanoFolder: 0.252 Positive Predictive Value CMfinder(seed): 0.774 NanoFolder: 0.188 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.486 Mastr(seed): 0.312 Sensitivity CMfinder(seed): 0.312 Mastr(seed): 0.118 Positive Predictive Value CMfinder(seed): 0.757 Mastr(seed): 0.828 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08
Afold	41 TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.799 Afold: 0.646 Sensitivity TurboFold(seed): 0.768 Afold: 0.650 Positive Predictive Value TurboFold(seed): 0.832 Afold: 0.644 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	699 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.748 Afold: 0.480 Sensitivity PETfold_pre2.0(seed): 0.686 Afold: 0.477 Positive Predictive Value PETfold_pre2.0(seed): 0.815 Afold: 0.484 Number of pairs reference - predicted secondary structure: 699 Wilcoxon single-rank test P-value: 3.56938820447e-08	1275 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.691 Afold: 0.434 Sensitivity ContextFold: 0.653 Afold: 0.433 Positive Predictive Value ContextFold: 0.733 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	348 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.780 Afold: 0.572 Sensitivity TurboFold(20): 0.730 Afold: 0.560 Positive Predictive Value TurboFold(20): 0.834 Afold: 0.586 Number of pairs reference - predicted secondary structure: 348 Wilcoxon single-rank test P-value: 3.56938820447e-08	576 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.751 Afold: 0.515 Sensitivity CentroidAlifold(seed): 0.625 Afold: 0.508 Positive Predictive Value CentroidAlifold(seed): 0.903 Afold: 0.522 Number of pairs reference - predicted secondary structure: 576 Wilcoxon single-rank test P-value: 3.56938820447e-08	418 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 Afold: 0.473 Sensitivity PETfold_pre2.0(20): 0.679 Afold: 0.469 Positive Predictive Value PETfold_pre2.0(20): 0.798 Afold: 0.479 Number of pairs reference - predicted secondary structure: 418 Wilcoxon single-rank test P-value: 3.56938820447e-08	421 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.731 Afold: 0.474 Sensitivity CentroidAlifold(20): 0.603 Afold: 0.470 Positive Predictive Value CentroidAlifold(20): 0.885 Afold: 0.479 Number of pairs reference - predicted secondary structure: 421 Wilcoxon single-rank test P-value: 3.56938820447e-08	1002 CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.664 Afold: 0.537 Sensitivity CentroidHomfold‑LAST: 0.525 Afold: 0.531 Positive Predictive Value CentroidHomfold‑LAST: 0.840 Afold: 0.545 Number of pairs reference - predicted secondary structure: 1002 Wilcoxon single-rank test P-value: 3.56938820447e-08	342 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.740 Afold: 0.556 Sensitivity PPfold(20): 0.631 Afold: 0.544 Positive Predictive Value PPfold(20): 0.869 Afold: 0.570 Number of pairs reference - predicted secondary structure: 342 Wilcoxon single-rank test P-value: 3.56938820447e-08	421 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.676 Afold: 0.474 Sensitivity RNAalifold(20): 0.589 Afold: 0.470 Positive Predictive Value RNAalifold(20): 0.775 Afold: 0.479 Number of pairs reference - predicted secondary structure: 421 Wilcoxon single-rank test P-value: 3.56938820447e-08	584 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.651 Afold: 0.515 Sensitivity MXScarna(seed): 0.564 Afold: 0.508 Positive Predictive Value MXScarna(seed): 0.752 Afold: 0.522 Number of pairs reference - predicted secondary structure: 584 Wilcoxon single-rank test P-value: 3.56938820447e-08	421 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.635 Afold: 0.474 Sensitivity MXScarna(20): 0.575 Afold: 0.470 Positive Predictive Value MXScarna(20): 0.702 Afold: 0.479 Number of pairs reference - predicted secondary structure: 421 Wilcoxon single-rank test P-value: 3.56938820447e-08	1274 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.556 Afold: 0.434 Sensitivity IPknot: 0.490 Afold: 0.434 Positive Predictive Value IPknot: 0.632 Afold: 0.435 Number of pairs reference - predicted secondary structure: 1274 Wilcoxon single-rank test P-value: 3.56938820447e-08	327 Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.666 Afold: 0.573 Sensitivity Multilign(20): 0.594 Afold: 0.560 Positive Predictive Value Multilign(20): 0.749 Afold: 0.587 Number of pairs reference - predicted secondary structure: 327 Wilcoxon single-rank test P-value: 3.56938820447e-08	292 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.598 Afold: 0.537 Sensitivity Murlet(20): 0.466 Afold: 0.528 Positive Predictive Value Murlet(20): 0.769 Afold: 0.548 Number of pairs reference - predicted secondary structure: 292 Wilcoxon single-rank test P-value: 3.56938820447e-08	580 RNAalifold(seed) vs Afold Matthews Correlation Coefficient RNAalifold(seed): 0.640 Afold: 0.509 Sensitivity RNAalifold(seed): 0.491 Afold: 0.503 Positive Predictive Value RNAalifold(seed): 0.835 Afold: 0.516 Number of pairs reference - predicted secondary structure: 580 Wilcoxon single-rank test P-value: 3.56938820447e-08	1238 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.530 Afold: 0.441 Sensitivity CentroidFold: 0.468 Afold: 0.441 Positive Predictive Value CentroidFold: 0.601 Afold: 0.443 Number of pairs reference - predicted secondary structure: 1238 Wilcoxon single-rank test P-value: 3.56938820447e-08	195 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.620 Afold: 0.613 Sensitivity RNASampler(20): 0.433 Afold: 0.606 Positive Predictive Value RNASampler(20): 0.889 Afold: 0.622 Number of pairs reference - predicted secondary structure: 195 Wilcoxon single-rank test P-value: 3.09925167801e-06	1275 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.516 Afold: 0.434 Sensitivity Contrafold: 0.497 Afold: 0.433 Positive Predictive Value Contrafold: 0.535 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	1275 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.482 Afold: 0.434 Sensitivity Sfold: 0.431 Afold: 0.433 Positive Predictive Value Sfold: 0.539 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.697 Afold: 0.589 Sensitivity Multilign(seed): 0.651 Afold: 0.592 Positive Predictive Value Multilign(seed): 0.747 Afold: 0.588 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	1275 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.470 Afold: 0.434 Sensitivity MaxExpect: 0.457 Afold: 0.433 Positive Predictive Value MaxExpect: 0.484 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	1275 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.464 Afold: 0.434 Sensitivity ProbKnot: 0.459 Afold: 0.433 Positive Predictive Value ProbKnot: 0.469 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	1275 Fold vs Afold Matthews Correlation Coefficient Fold: 0.443 Afold: 0.434 Sensitivity Fold: 0.446 Afold: 0.433 Positive Predictive Value Fold: 0.440 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	90 RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.634 Afold: 0.602 Sensitivity RNASampler(seed): 0.471 Afold: 0.593 Positive Predictive Value RNASampler(seed): 0.856 Afold: 0.615 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 3.56938820447e-08	1275 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.446 Afold: 0.434 Sensitivity UNAFold: 0.444 Afold: 0.433 Positive Predictive Value UNAFold: 0.450 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	1002 RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.553 Afold: 0.537 Sensitivity RNAsubopt: 0.553 Afold: 0.531 Positive Predictive Value RNAsubopt: 0.554 Afold: 0.545 Number of pairs reference - predicted secondary structure: 1002 Wilcoxon single-rank test P-value: 3.56938820447e-08	421 Afold vs RSpredict(20) Matthews Correlation Coefficient Afold: 0.474 RSpredict(20): 0.460 Sensitivity Afold: 0.470 RSpredict(20): 0.378 Positive Predictive Value Afold: 0.479 RSpredict(20): 0.562 Number of pairs reference - predicted secondary structure: 421 Wilcoxon single-rank test P-value: 5.62644058675e-08	346 Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.572 CMfinder(20): 0.534 Sensitivity Afold: 0.559 CMfinder(20): 0.365 Positive Predictive Value Afold: 0.586 CMfinder(20): 0.783 Number of pairs reference - predicted secondary structure: 346 Wilcoxon single-rank test P-value: 3.56938820447e-08	1199 PknotsRG vs Afold Matthews Correlation Coefficient PknotsRG: 0.467 Afold: 0.463 Sensitivity PknotsRG: 0.465 Afold: 0.460 Positive Predictive Value PknotsRG: 0.469 Afold: 0.467 Number of pairs reference - predicted secondary structure: 1199 Wilcoxon single-rank test P-value: 3.56938820447e-08	421 Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.501 Afold: 0.474 Sensitivity Carnac(20): 0.281 Afold: 0.470 Positive Predictive Value Carnac(20): 0.893 Afold: 0.479 Number of pairs reference - predicted secondary structure: 421 Wilcoxon single-rank test P-value: 3.56938820447e-08	1275 RNAfold vs Afold Matthews Correlation Coefficient RNAfold: 0.436 Afold: 0.434 Sensitivity RNAfold: 0.437 Afold: 0.433 Positive Predictive Value RNAfold: 0.435 Afold: 0.434 Number of pairs reference - predicted secondary structure: 1275 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 Afold vs CMfinder(seed) Matthews Correlation Coefficient Afold: 0.616 CMfinder(seed): 0.489 Sensitivity Afold: 0.610 CMfinder(seed): 0.317 Positive Predictive Value Afold: 0.624 CMfinder(seed): 0.755 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08		- HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.623 Afold: 0.559 Sensitivity HotKnots: 0.603 Afold: 0.542 Positive Predictive Value HotKnots: 0.650 Afold: 0.583 Number of pairs reference - predicted secondary structure: 527 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.461 CRWrnafold: 0.437 Sensitivity Afold: 0.458 CRWrnafold: 0.438 Positive Predictive Value Afold: 0.464 CRWrnafold: 0.438 Number of pairs reference - predicted secondary structure: 1171 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Afold vs Pknots Matthews Correlation Coefficient Afold: 0.540 Pknots: 0.537 Sensitivity Afold: 0.519 Pknots: 0.511 Positive Predictive Value Afold: 0.572 Pknots: 0.575 Number of pairs reference - predicted secondary structure: 404 Wilcoxon single-rank test P-value: 0.0274981398492	+ Afold vs McQFold Matthews Correlation Coefficient Afold: 0.519 McQFold: 0.460 Sensitivity Afold: 0.517 McQFold: 0.447 Positive Predictive Value Afold: 0.523 McQFold: 0.475 Number of pairs reference - predicted secondary structure: 1061 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.539 RNAshapes: 0.514 Sensitivity Afold: 0.532 RNAshapes: 0.504 Positive Predictive Value Afold: 0.548 RNAshapes: 0.528 Number of pairs reference - predicted secondary structure: 967 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs Afold Matthews Correlation Coefficient PPfold(seed): 0.685 Afold: 0.638 Sensitivity PPfold(seed): 0.581 Afold: 0.642 Positive Predictive Value PPfold(seed): 0.808 Afold: 0.636 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Mastr(20) Matthews Correlation Coefficient Afold: 0.477 Mastr(20): 0.236 Sensitivity Afold: 0.474 Mastr(20): 0.071 Positive Predictive Value Afold: 0.480 Mastr(20): 0.782 Number of pairs reference - predicted secondary structure: 373 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.595 Murlet(seed): 0.553 Sensitivity Afold: 0.589 Murlet(seed): 0.371 Positive Predictive Value Afold: 0.601 Murlet(seed): 0.823 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.541 RNASLOpt: 0.467 Sensitivity Afold: 0.534 RNASLOpt: 0.434 Positive Predictive Value Afold: 0.550 RNASLOpt: 0.505 Number of pairs reference - predicted secondary structure: 944 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.580 Cylofold: 0.540 Sensitivity Afold: 0.561 Cylofold: 0.503 Positive Predictive Value Afold: 0.607 Cylofold: 0.588 Number of pairs reference - predicted secondary structure: 481 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.482 RNAwolf: 0.339 Sensitivity Afold: 0.479 RNAwolf: 0.352 Positive Predictive Value Afold: 0.486 RNAwolf: 0.328 Number of pairs reference - predicted secondary structure: 1126 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.538 Vsfold4: 0.344 Sensitivity Afold: 0.531 Vsfold4: 0.313 Positive Predictive Value Afold: 0.546 Vsfold4: 0.380 Number of pairs reference - predicted secondary structure: 978 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.539 Vsfold5: 0.335 Sensitivity Afold: 0.532 Vsfold5: 0.314 Positive Predictive Value Afold: 0.548 Vsfold5: 0.361 Number of pairs reference - predicted secondary structure: 971 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Alterna Matthews Correlation Coefficient Afold: 0.542 Alterna: 0.531 Sensitivity Afold: 0.522 Alterna: 0.509 Positive Predictive Value Afold: 0.574 Alterna: 0.565 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.542 RDfolder: 0.482 Sensitivity Afold: 0.522 RDfolder: 0.417 Positive Predictive Value Afold: 0.574 RDfolder: 0.569 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.575 Carnac(seed): 0.258 Sensitivity Afold: 0.577 Carnac(seed): 0.076 Positive Predictive Value Afold: 0.574 Carnac(seed): 0.880 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.556 MCFold: 0.482 Sensitivity Afold: 0.538 MCFold: 0.521 Positive Predictive Value Afold: 0.581 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 472 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.517 RSpredict(seed): 0.386 Sensitivity Afold: 0.511 RSpredict(seed): 0.244 Positive Predictive Value Afold: 0.524 RSpredict(seed): 0.612 Number of pairs reference - predicted secondary structure: 572 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.559 NanoFolder: 0.188 Sensitivity Afold: 0.551 NanoFolder: 0.218 Positive Predictive Value Afold: 0.569 NanoFolder: 0.165 Number of pairs reference - predicted secondary structure: 160 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.564 Mastr(seed): 0.123 Sensitivity Afold: 0.559 Mastr(seed): 0.019 Positive Predictive Value Afold: 0.571 Mastr(seed): 0.821 Number of pairs reference - predicted secondary structure: 502 Wilcoxon single-rank test P-value: 3.56938820447e-08
HotKnots	33 TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.798 HotKnots: 0.740 Sensitivity TurboFold(seed): 0.766 HotKnots: 0.745 Positive Predictive Value TurboFold(seed): 0.835 HotKnots: 0.740 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	495 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 HotKnots: 0.657 Sensitivity PETfold_pre2.0(seed): 0.826 HotKnots: 0.660 Positive Predictive Value PETfold_pre2.0(seed): 0.938 HotKnots: 0.659 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.778 HotKnots: 0.613 Sensitivity ContextFold: 0.740 HotKnots: 0.607 Positive Predictive Value ContextFold: 0.822 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.889 HotKnots: 0.698 Sensitivity TurboFold(20): 0.861 HotKnots: 0.695 Positive Predictive Value TurboFold(20): 0.919 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	213 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.789 HotKnots: 0.687 Sensitivity CentroidAlifold(seed): 0.698 HotKnots: 0.688 Positive Predictive Value CentroidAlifold(seed): 0.895 HotKnots: 0.691 Number of pairs reference - predicted secondary structure: 213 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 HotKnots: 0.698 Sensitivity PETfold_pre2.0(20): 0.737 HotKnots: 0.695 Positive Predictive Value PETfold_pre2.0(20): 0.975 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.849 HotKnots: 0.698 Sensitivity CentroidAlifold(20): 0.754 HotKnots: 0.695 Positive Predictive Value CentroidAlifold(20): 0.957 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.735 HotKnots: 0.613 Sensitivity CentroidHomfold‑LAST: 0.665 HotKnots: 0.607 Positive Predictive Value CentroidHomfold‑LAST: 0.815 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.839 HotKnots: 0.696 Sensitivity PPfold(20): 0.721 HotKnots: 0.692 Positive Predictive Value PPfold(20): 0.977 HotKnots: 0.704 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.816 HotKnots: 0.698 Sensitivity RNAalifold(20): 0.690 HotKnots: 0.695 Positive Predictive Value RNAalifold(20): 0.966 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	230 MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.751 HotKnots: 0.677 Sensitivity MXScarna(seed): 0.714 HotKnots: 0.678 Positive Predictive Value MXScarna(seed): 0.792 HotKnots: 0.680 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.838 HotKnots: 0.698 Sensitivity MXScarna(20): 0.791 HotKnots: 0.695 Positive Predictive Value MXScarna(20): 0.891 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.692 HotKnots: 0.613 Sensitivity IPknot: 0.659 HotKnots: 0.607 Positive Predictive Value IPknot: 0.730 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs HotKnots Matthews Correlation Coefficient Multilign(20): 0.784 HotKnots: 0.696 Sensitivity Multilign(20): 0.697 HotKnots: 0.692 Positive Predictive Value Multilign(20): 0.885 HotKnots: 0.703 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.750 HotKnots: 0.699 Sensitivity Murlet(20): 0.619 HotKnots: 0.696 Positive Predictive Value Murlet(20): 0.913 HotKnots: 0.706 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	202 HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: 0.695 RNAalifold(seed): 0.605 Sensitivity HotKnots: 0.694 RNAalifold(seed): 0.399 Positive Predictive Value HotKnots: 0.701 RNAalifold(seed): 0.921 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.645 HotKnots: 0.613 Sensitivity CentroidFold: 0.612 HotKnots: 0.607 Positive Predictive Value CentroidFold: 0.685 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.770 HotKnots: 0.698 Sensitivity RNASampler(20): 0.622 HotKnots: 0.694 Positive Predictive Value RNASampler(20): 0.957 HotKnots: 0.706 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.644 HotKnots: 0.613 Sensitivity Contrafold: 0.635 HotKnots: 0.607 Positive Predictive Value Contrafold: 0.658 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.617 HotKnots: 0.613 Sensitivity Sfold: 0.581 HotKnots: 0.607 Positive Predictive Value Sfold: 0.662 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.519 Multilign(seed): 0.485 Sensitivity HotKnots: 0.521 Multilign(seed): 0.386 Positive Predictive Value HotKnots: 0.526 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.94492482736e-08	876 MaxExpect vs HotKnots Matthews Correlation Coefficient MaxExpect: 0.634 HotKnots: 0.613 Sensitivity MaxExpect: 0.618 HotKnots: 0.607 Positive Predictive Value MaxExpect: 0.655 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 ProbKnot vs HotKnots Matthews Correlation Coefficient ProbKnot: 0.632 HotKnots: 0.613 Sensitivity ProbKnot: 0.623 HotKnots: 0.607 Positive Predictive Value ProbKnot: 0.645 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.630 HotKnots: 0.613 Sensitivity Fold: 0.622 HotKnots: 0.607 Positive Predictive Value Fold: 0.643 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	84 RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.537 HotKnots: 0.536 Sensitivity RNASampler(seed): 0.372 HotKnots: 0.524 Positive Predictive Value RNASampler(seed): 0.780 HotKnots: 0.553 Number of pairs reference - predicted secondary structure: 84 Wilcoxon single-rank test P-value: 1.0	876 UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.618 HotKnots: 0.613 Sensitivity UNAFold: 0.603 HotKnots: 0.607 Positive Predictive Value UNAFold: 0.638 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 RNAsubopt vs HotKnots Matthews Correlation Coefficient RNAsubopt: 0.615 HotKnots: 0.613 Sensitivity RNAsubopt: 0.609 HotKnots: 0.607 Positive Predictive Value RNAsubopt: 0.626 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 7.14263132478e-06	320 RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): 0.789 HotKnots: 0.698 Sensitivity RSpredict(20): 0.693 HotKnots: 0.695 Positive Predictive Value RSpredict(20): 0.901 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs HotKnots Matthews Correlation Coefficient CMfinder(20): 0.735 HotKnots: 0.696 Sensitivity CMfinder(20): 0.603 HotKnots: 0.693 Positive Predictive Value CMfinder(20): 0.899 HotKnots: 0.703 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 PknotsRG vs HotKnots Matthews Correlation Coefficient PknotsRG: 0.618 HotKnots: 0.613 Sensitivity PknotsRG: 0.610 HotKnots: 0.607 Positive Predictive Value PknotsRG: 0.630 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 HotKnots vs Carnac(20) Matthews Correlation Coefficient HotKnots: 0.698 Carnac(20): 0.675 Sensitivity HotKnots: 0.695 Carnac(20): 0.500 Positive Predictive Value HotKnots: 0.705 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.613 RNAfold: 0.612 Sensitivity HotKnots: 0.607 RNAfold: 0.604 Positive Predictive Value HotKnots: 0.624 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 0.041044797429	76 CMfinder(seed) vs HotKnots Matthews Correlation Coefficient CMfinder(seed): 0.582 HotKnots: 0.503 Sensitivity CMfinder(seed): 0.446 HotKnots: 0.492 Positive Predictive Value CMfinder(seed): 0.765 HotKnots: 0.521 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	527 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.623 Afold: 0.559 Sensitivity HotKnots: 0.603 Afold: 0.542 Positive Predictive Value HotKnots: 0.650 Afold: 0.583 Number of pairs reference - predicted secondary structure: 527 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CRWrnafold vs HotKnots Matthews Correlation Coefficient CRWrnafold: 0.632 HotKnots: 0.613 Sensitivity CRWrnafold: 0.620 HotKnots: 0.607 Positive Predictive Value CRWrnafold: 0.650 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs HotKnots Matthews Correlation Coefficient Pknots: 0.606 HotKnots: 0.593 Sensitivity Pknots: 0.595 HotKnots: 0.589 Positive Predictive Value Pknots: 0.624 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.613 McQFold: 0.583 Sensitivity HotKnots: 0.607 McQFold: 0.557 Positive Predictive Value HotKnots: 0.624 McQFold: 0.615 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	= HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.613 RNAshapes: 0.612 Sensitivity HotKnots: 0.607 RNAshapes: 0.603 Positive Predictive Value HotKnots: 0.624 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 0.581569793731	+ HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.702 PPfold(seed): 0.380 Sensitivity HotKnots: 0.713 PPfold(seed): 0.170 Positive Predictive Value HotKnots: 0.697 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Mastr(20) vs HotKnots Matthews Correlation Coefficient Mastr(20): 0.708 HotKnots: 0.698 Sensitivity Mastr(20): 0.635 HotKnots: 0.695 Positive Predictive Value Mastr(20): 0.793 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 2.12176083234e-07	+ HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.572 Murlet(seed): 0.477 Sensitivity HotKnots: 0.562 Murlet(seed): 0.277 Positive Predictive Value HotKnots: 0.588 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.613 RNASLOpt: 0.562 Sensitivity HotKnots: 0.607 RNASLOpt: 0.520 Positive Predictive Value HotKnots: 0.624 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.638 Cylofold: 0.577 Sensitivity HotKnots: 0.631 Cylofold: 0.554 Positive Predictive Value HotKnots: 0.651 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.613 RNAwolf: 0.518 Sensitivity HotKnots: 0.607 RNAwolf: 0.523 Positive Predictive Value HotKnots: 0.624 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.613 Vsfold4: 0.486 Sensitivity HotKnots: 0.607 Vsfold4: 0.446 Positive Predictive Value HotKnots: 0.624 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.613 Vsfold5: 0.477 Sensitivity HotKnots: 0.607 Vsfold5: 0.450 Positive Predictive Value HotKnots: 0.624 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.594 Alterna: 0.552 Sensitivity HotKnots: 0.590 Alterna: 0.547 Positive Predictive Value HotKnots: 0.605 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.594 RDfolder: 0.520 Sensitivity HotKnots: 0.590 RDfolder: 0.464 Positive Predictive Value HotKnots: 0.605 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.619 Carnac(seed): 0.414 Sensitivity HotKnots: 0.615 Carnac(seed): 0.197 Positive Predictive Value HotKnots: 0.629 Carnac(seed): 0.875 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.614 MCFold: 0.473 Sensitivity HotKnots: 0.606 MCFold: 0.524 Positive Predictive Value HotKnots: 0.627 MCFold: 0.434 Number of pairs reference - predicted secondary structure: 760 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.687 RSpredict(seed): 0.379 Sensitivity HotKnots: 0.688 RSpredict(seed): 0.256 Positive Predictive Value HotKnots: 0.691 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 213 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.656 NanoFolder: 0.339 Sensitivity HotKnots: 0.650 NanoFolder: 0.391 Positive Predictive Value HotKnots: 0.668 NanoFolder: 0.302 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.677 Mastr(seed): 0.266 Sensitivity HotKnots: 0.677 Mastr(seed): 0.091 Positive Predictive Value HotKnots: 0.680 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 231 Wilcoxon single-rank test P-value: 3.56938820447e-08
CRWrnafold	51 TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.791 CRWrnafold: 0.580 Sensitivity TurboFold(seed): 0.762 CRWrnafold: 0.585 Positive Predictive Value TurboFold(seed): 0.822 CRWrnafold: 0.577 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1170 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.747 CRWrnafold: 0.486 Sensitivity PETfold_pre2.0(seed): 0.672 CRWrnafold: 0.486 Positive Predictive Value PETfold_pre2.0(seed): 0.832 CRWrnafold: 0.487 Number of pairs reference - predicted secondary structure: 1170 Wilcoxon single-rank test P-value: 3.56938820447e-08	1837 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.729 CRWrnafold: 0.437 Sensitivity ContextFold: 0.691 CRWrnafold: 0.440 Positive Predictive Value ContextFold: 0.770 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.787 CRWrnafold: 0.542 Sensitivity TurboFold(20): 0.740 CRWrnafold: 0.533 Positive Predictive Value TurboFold(20): 0.837 CRWrnafold: 0.553 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	671 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.748 CRWrnafold: 0.508 Sensitivity CentroidAlifold(seed): 0.618 CRWrnafold: 0.503 Positive Predictive Value CentroidAlifold(seed): 0.905 CRWrnafold: 0.514 Number of pairs reference - predicted secondary structure: 671 Wilcoxon single-rank test P-value: 3.56938820447e-08	587 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.784 CRWrnafold: 0.540 Sensitivity PETfold_pre2.0(20): 0.712 CRWrnafold: 0.531 Positive Predictive Value PETfold_pre2.0(20): 0.864 CRWrnafold: 0.550 Number of pairs reference - predicted secondary structure: 587 Wilcoxon single-rank test P-value: 3.56938820447e-08	590 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.779 CRWrnafold: 0.541 Sensitivity CentroidAlifold(20): 0.658 CRWrnafold: 0.532 Positive Predictive Value CentroidAlifold(20): 0.923 CRWrnafold: 0.551 Number of pairs reference - predicted secondary structure: 590 Wilcoxon single-rank test P-value: 3.56938820447e-08	1640 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 CRWrnafold: 0.480 Sensitivity CentroidHomfold‑LAST: 0.527 CRWrnafold: 0.481 Positive Predictive Value CentroidHomfold‑LAST: 0.850 CRWrnafold: 0.482 Number of pairs reference - predicted secondary structure: 1640 Wilcoxon single-rank test P-value: 3.56938820447e-08	554 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.762 CRWrnafold: 0.545 Sensitivity PPfold(20): 0.656 CRWrnafold: 0.536 Positive Predictive Value PPfold(20): 0.885 CRWrnafold: 0.556 Number of pairs reference - predicted secondary structure: 554 Wilcoxon single-rank test P-value: 3.56938820447e-08	590 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.738 CRWrnafold: 0.541 Sensitivity RNAalifold(20): 0.631 CRWrnafold: 0.532 Positive Predictive Value RNAalifold(20): 0.865 CRWrnafold: 0.551 Number of pairs reference - predicted secondary structure: 590 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.662 CRWrnafold: 0.509 Sensitivity MXScarna(seed): 0.571 CRWrnafold: 0.504 Positive Predictive Value MXScarna(seed): 0.769 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	590 MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.699 CRWrnafold: 0.541 Sensitivity MXScarna(20): 0.633 CRWrnafold: 0.532 Positive Predictive Value MXScarna(20): 0.772 CRWrnafold: 0.551 Number of pairs reference - predicted secondary structure: 590 Wilcoxon single-rank test P-value: 3.56938820447e-08	1837 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.587 CRWrnafold: 0.437 Sensitivity IPknot: 0.526 CRWrnafold: 0.440 Positive Predictive Value IPknot: 0.655 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.685 CRWrnafold: 0.546 Sensitivity Multilign(20): 0.617 CRWrnafold: 0.537 Positive Predictive Value Multilign(20): 0.762 CRWrnafold: 0.557 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.638 CRWrnafold: 0.546 Sensitivity Murlet(20): 0.506 CRWrnafold: 0.538 Positive Predictive Value Murlet(20): 0.806 CRWrnafold: 0.556 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	661 RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.620 CRWrnafold: 0.507 Sensitivity RNAalifold(seed): 0.444 CRWrnafold: 0.502 Positive Predictive Value RNAalifold(seed): 0.868 CRWrnafold: 0.514 Number of pairs reference - predicted secondary structure: 661 Wilcoxon single-rank test P-value: 3.56938820447e-08	1837 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.554 CRWrnafold: 0.437 Sensitivity CentroidFold: 0.497 CRWrnafold: 0.440 Positive Predictive Value CentroidFold: 0.619 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.676 CRWrnafold: 0.609 Sensitivity RNASampler(20): 0.522 CRWrnafold: 0.605 Positive Predictive Value RNASampler(20): 0.877 CRWrnafold: 0.614 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1837 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.542 CRWrnafold: 0.437 Sensitivity Contrafold: 0.526 CRWrnafold: 0.440 Positive Predictive Value Contrafold: 0.559 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	1837 Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.510 CRWrnafold: 0.437 Sensitivity Sfold: 0.461 CRWrnafold: 0.440 Positive Predictive Value Sfold: 0.565 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.681 CRWrnafold: 0.453 Sensitivity Multilign(seed): 0.649 CRWrnafold: 0.465 Positive Predictive Value Multilign(seed): 0.717 CRWrnafold: 0.445 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	1837 MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.504 CRWrnafold: 0.437 Sensitivity MaxExpect: 0.491 CRWrnafold: 0.440 Positive Predictive Value MaxExpect: 0.518 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	1837 ProbKnot vs CRWrnafold Matthews Correlation Coefficient ProbKnot: 0.500 CRWrnafold: 0.437 Sensitivity ProbKnot: 0.497 CRWrnafold: 0.440 Positive Predictive Value ProbKnot: 0.505 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	1837 Fold vs CRWrnafold Matthews Correlation Coefficient Fold: 0.479 CRWrnafold: 0.437 Sensitivity Fold: 0.483 CRWrnafold: 0.440 Positive Predictive Value Fold: 0.477 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.629 CRWrnafold: 0.473 Sensitivity RNASampler(seed): 0.468 CRWrnafold: 0.465 Positive Predictive Value RNASampler(seed): 0.847 CRWrnafold: 0.485 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	1837 UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.477 CRWrnafold: 0.437 Sensitivity UNAFold: 0.474 CRWrnafold: 0.440 Positive Predictive Value UNAFold: 0.481 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	1640 RNAsubopt vs CRWrnafold Matthews Correlation Coefficient RNAsubopt: 0.525 CRWrnafold: 0.480 Sensitivity RNAsubopt: 0.530 CRWrnafold: 0.481 Positive Predictive Value RNAsubopt: 0.521 CRWrnafold: 0.482 Number of pairs reference - predicted secondary structure: 1640 Wilcoxon single-rank test P-value: 3.56938820447e-08	590 RSpredict(20) vs CRWrnafold Matthews Correlation Coefficient RSpredict(20): 0.567 CRWrnafold: 0.541 Sensitivity RSpredict(20): 0.442 CRWrnafold: 0.532 Positive Predictive Value RSpredict(20): 0.727 CRWrnafold: 0.551 Number of pairs reference - predicted secondary structure: 590 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 CMfinder(20) vs CRWrnafold Matthews Correlation Coefficient CMfinder(20): 0.549 CRWrnafold: 0.541 Sensitivity CMfinder(20): 0.380 CRWrnafold: 0.532 Positive Predictive Value CMfinder(20): 0.794 CRWrnafold: 0.552 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	1837 PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.469 CRWrnafold: 0.437 Sensitivity PknotsRG: 0.470 CRWrnafold: 0.440 Positive Predictive Value PknotsRG: 0.468 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	590 CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.541 Carnac(20): 0.510 Sensitivity CRWrnafold: 0.532 Carnac(20): 0.289 Positive Predictive Value CRWrnafold: 0.551 Carnac(20): 0.900 Number of pairs reference - predicted secondary structure: 590 Wilcoxon single-rank test P-value: 3.56938820447e-08	1837 RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.468 CRWrnafold: 0.437 Sensitivity RNAfold: 0.470 CRWrnafold: 0.440 Positive Predictive Value RNAfold: 0.468 CRWrnafold: 0.435 Number of pairs reference - predicted secondary structure: 1837 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: 0.556 CMfinder(seed): 0.486 Sensitivity CRWrnafold: 0.554 CMfinder(seed): 0.312 Positive Predictive Value CRWrnafold: 0.559 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	1171 Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.461 CRWrnafold: 0.437 Sensitivity Afold: 0.458 CRWrnafold: 0.438 Positive Predictive Value Afold: 0.464 CRWrnafold: 0.438 Number of pairs reference - predicted secondary structure: 1171 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 CRWrnafold vs HotKnots Matthews Correlation Coefficient CRWrnafold: 0.632 HotKnots: 0.613 Sensitivity CRWrnafold: 0.620 HotKnots: 0.607 Positive Predictive Value CRWrnafold: 0.650 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.614 Pknots: 0.606 Sensitivity CRWrnafold: 0.600 Pknots: 0.595 Positive Predictive Value CRWrnafold: 0.634 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 696 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CRWrnafold vs McQFold Matthews Correlation Coefficient CRWrnafold: 0.468 McQFold: 0.467 Sensitivity CRWrnafold: 0.471 McQFold: 0.457 Positive Predictive Value CRWrnafold: 0.466 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1706 Wilcoxon single-rank test P-value: 0.0853441262641	+ CRWrnafold vs RNAshapes Matthews Correlation Coefficient CRWrnafold: 0.484 RNAshapes: 0.477 Sensitivity CRWrnafold: 0.483 RNAshapes: 0.472 Positive Predictive Value CRWrnafold: 0.486 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1587 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs CRWrnafold Matthews Correlation Coefficient PPfold(seed): 0.626 CRWrnafold: 0.565 Sensitivity PPfold(seed): 0.495 CRWrnafold: 0.572 Positive Predictive Value PPfold(seed): 0.794 CRWrnafold: 0.559 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.538 Mastr(20): 0.348 Sensitivity CRWrnafold: 0.529 Mastr(20): 0.154 Positive Predictive Value CRWrnafold: 0.549 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 566 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.540 CRWrnafold: 0.513 Sensitivity Murlet(seed): 0.360 CRWrnafold: 0.507 Positive Predictive Value Murlet(seed): 0.811 CRWrnafold: 0.520 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 6.06606238843e-08	+ CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.487 RNASLOpt: 0.470 Sensitivity CRWrnafold: 0.486 RNASLOpt: 0.442 Positive Predictive Value CRWrnafold: 0.489 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1542 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.665 Cylofold: 0.574 Sensitivity CRWrnafold: 0.649 Cylofold: 0.551 Positive Predictive Value CRWrnafold: 0.686 Cylofold: 0.605 Number of pairs reference - predicted secondary structure: 797 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.440 RNAwolf: 0.343 Sensitivity CRWrnafold: 0.444 RNAwolf: 0.358 Positive Predictive Value CRWrnafold: 0.438 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1787 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.481 Vsfold4: 0.346 Sensitivity CRWrnafold: 0.482 Vsfold4: 0.318 Positive Predictive Value CRWrnafold: 0.483 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1611 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.482 Vsfold5: 0.339 Sensitivity CRWrnafold: 0.482 Vsfold5: 0.322 Positive Predictive Value CRWrnafold: 0.484 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1601 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.615 Alterna: 0.552 Sensitivity CRWrnafold: 0.601 Alterna: 0.546 Positive Predictive Value CRWrnafold: 0.635 Alterna: 0.565 Number of pairs reference - predicted secondary structure: 692 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.615 RDfolder: 0.520 Sensitivity CRWrnafold: 0.601 RDfolder: 0.464 Positive Predictive Value CRWrnafold: 0.635 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 692 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.504 Carnac(seed): 0.215 Sensitivity CRWrnafold: 0.507 Carnac(seed): 0.055 Positive Predictive Value CRWrnafold: 0.503 Carnac(seed): 0.850 Number of pairs reference - predicted secondary structure: 268 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.629 MCFold: 0.473 Sensitivity CRWrnafold: 0.614 MCFold: 0.524 Positive Predictive Value CRWrnafold: 0.649 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 760 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.509 RSpredict(seed): 0.341 Sensitivity CRWrnafold: 0.504 RSpredict(seed): 0.188 Positive Predictive Value CRWrnafold: 0.516 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 670 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.505 NanoFolder: 0.194 Sensitivity CRWrnafold: 0.503 NanoFolder: 0.229 Positive Predictive Value CRWrnafold: 0.509 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.509 Mastr(seed): 0.115 Sensitivity CRWrnafold: 0.505 Mastr(seed): 0.016 Positive Predictive Value CRWrnafold: 0.514 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08
Pknots	25 TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.711 Pknots: 0.628 Sensitivity TurboFold(seed): 0.662 Pknots: 0.632 Positive Predictive Value TurboFold(seed): 0.768 Pknots: 0.630 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	360 PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 Pknots: 0.666 Sensitivity PETfold_pre2.0(seed): 0.870 Pknots: 0.673 Positive Predictive Value PETfold_pre2.0(seed): 0.950 Pknots: 0.663 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.763 Pknots: 0.606 Sensitivity ContextFold: 0.721 Pknots: 0.595 Positive Predictive Value ContextFold: 0.811 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.910 Pknots: 0.655 Sensitivity TurboFold(20): 0.885 Pknots: 0.662 Positive Predictive Value TurboFold(20): 0.937 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	146 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.780 Pknots: 0.509 Sensitivity CentroidAlifold(seed): 0.673 Pknots: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.906 Pknots: 0.523 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.885 Pknots: 0.655 Sensitivity PETfold_pre2.0(20): 0.807 Pknots: 0.662 Positive Predictive Value PETfold_pre2.0(20): 0.972 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.906 Pknots: 0.655 Sensitivity CentroidAlifold(20): 0.843 Pknots: 0.662 Positive Predictive Value CentroidAlifold(20): 0.974 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.745 Pknots: 0.606 Sensitivity CentroidHomfold‑LAST: 0.685 Pknots: 0.595 Positive Predictive Value CentroidHomfold‑LAST: 0.815 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.882 Pknots: 0.664 Sensitivity PPfold(20): 0.796 Pknots: 0.671 Positive Predictive Value PPfold(20): 0.979 Pknots: 0.662 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.881 Pknots: 0.655 Sensitivity RNAalifold(20): 0.794 Pknots: 0.662 Positive Predictive Value RNAalifold(20): 0.980 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	157 MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.748 Pknots: 0.532 Sensitivity MXScarna(seed): 0.715 Pknots: 0.527 Positive Predictive Value MXScarna(seed): 0.787 Pknots: 0.545 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.872 Pknots: 0.655 Sensitivity MXScarna(20): 0.834 Pknots: 0.662 Positive Predictive Value MXScarna(20): 0.913 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.687 Pknots: 0.606 Sensitivity IPknot: 0.652 Pknots: 0.595 Positive Predictive Value IPknot: 0.729 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	210 Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.827 Pknots: 0.656 Sensitivity Multilign(20): 0.757 Pknots: 0.662 Positive Predictive Value Multilign(20): 0.906 Pknots: 0.654 Number of pairs reference - predicted secondary structure: 210 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.780 Pknots: 0.657 Sensitivity Murlet(20): 0.685 Pknots: 0.663 Positive Predictive Value Murlet(20): 0.892 Pknots: 0.655 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.618 Pknots: 0.488 Sensitivity RNAalifold(seed): 0.420 Pknots: 0.481 Positive Predictive Value RNAalifold(seed): 0.914 Pknots: 0.503 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.656 Pknots: 0.606 Sensitivity CentroidFold: 0.620 Pknots: 0.595 Positive Predictive Value CentroidFold: 0.701 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.857 Pknots: 0.660 Sensitivity RNASampler(20): 0.758 Pknots: 0.666 Positive Predictive Value RNASampler(20): 0.971 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.656 Pknots: 0.606 Sensitivity Contrafold: 0.645 Pknots: 0.595 Positive Predictive Value Contrafold: 0.673 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs Sfold Matthews Correlation Coefficient Pknots: 0.606 Sfold: 0.601 Sensitivity Pknots: 0.595 Sfold: 0.565 Positive Predictive Value Pknots: 0.624 Sfold: 0.648 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 5.19883461079e-06	13 Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.699 Multilign(seed): 0.485 Sensitivity Pknots: 0.684 Multilign(seed): 0.386 Positive Predictive Value Pknots: 0.721 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	697 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.640 Pknots: 0.606 Sensitivity MaxExpect: 0.621 Pknots: 0.595 Positive Predictive Value MaxExpect: 0.666 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.639 Pknots: 0.606 Sensitivity ProbKnot: 0.631 Pknots: 0.595 Positive Predictive Value ProbKnot: 0.655 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Fold vs Pknots Matthews Correlation Coefficient Fold: 0.633 Pknots: 0.606 Sensitivity Fold: 0.622 Pknots: 0.595 Positive Predictive Value Fold: 0.650 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): 0.455 Pknots: 0.446 Sensitivity RNASampler(seed): 0.284 Pknots: 0.429 Positive Predictive Value RNASampler(seed): 0.738 Pknots: 0.475 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 2.71856013146e-06	697 Pknots vs UNAFold Matthews Correlation Coefficient Pknots: 0.606 UNAFold: 0.596 Sensitivity Pknots: 0.595 UNAFold: 0.583 Positive Predictive Value Pknots: 0.624 UNAFold: 0.616 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.608 Pknots: 0.606 Sensitivity RNAsubopt: 0.602 Pknots: 0.595 Positive Predictive Value RNAsubopt: 0.620 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 0.028456752624	212 RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.821 Pknots: 0.655 Sensitivity RSpredict(20): 0.738 Pknots: 0.662 Positive Predictive Value RSpredict(20): 0.915 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.791 Pknots: 0.655 Sensitivity CMfinder(20): 0.678 Pknots: 0.662 Positive Predictive Value CMfinder(20): 0.926 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs PknotsRG Matthews Correlation Coefficient Pknots: 0.606 PknotsRG: 0.603 Sensitivity Pknots: 0.595 PknotsRG: 0.595 Positive Predictive Value Pknots: 0.624 PknotsRG: 0.617 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 0.000349712763079	212 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.742 Pknots: 0.655 Sensitivity Carnac(20): 0.588 Pknots: 0.662 Positive Predictive Value Carnac(20): 0.940 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs RNAfold Matthews Correlation Coefficient Pknots: 0.606 RNAfold: 0.596 Sensitivity Pknots: 0.595 RNAfold: 0.588 Positive Predictive Value Pknots: 0.624 RNAfold: 0.611 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 CMfinder(seed) vs Pknots Matthews Correlation Coefficient CMfinder(seed): 0.512 Pknots: 0.398 Sensitivity CMfinder(seed): 0.382 Pknots: 0.381 Positive Predictive Value CMfinder(seed): 0.696 Pknots: 0.429 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	404 Afold vs Pknots Matthews Correlation Coefficient Afold: 0.540 Pknots: 0.537 Sensitivity Afold: 0.519 Pknots: 0.511 Positive Predictive Value Afold: 0.572 Pknots: 0.575 Number of pairs reference - predicted secondary structure: 404 Wilcoxon single-rank test P-value: 0.0274981398492	697 Pknots vs HotKnots Matthews Correlation Coefficient Pknots: 0.606 HotKnots: 0.593 Sensitivity Pknots: 0.595 HotKnots: 0.589 Positive Predictive Value Pknots: 0.624 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	696 CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.614 Pknots: 0.606 Sensitivity CRWrnafold: 0.600 Pknots: 0.595 Positive Predictive Value CRWrnafold: 0.634 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 696 Wilcoxon single-rank test P-value: 3.56938820447e-08		- McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.650 Pknots: 0.606 Sensitivity McQFold: 0.621 Pknots: 0.595 Positive Predictive Value McQFold: 0.686 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: 0.606 RNAshapes: 0.594 Sensitivity Pknots: 0.595 RNAshapes: 0.585 Positive Predictive Value Pknots: 0.624 RNAshapes: 0.610 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.646 PPfold(seed): 0.488 Sensitivity Pknots: 0.645 PPfold(seed): 0.281 Positive Predictive Value Pknots: 0.653 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.727 Pknots: 0.655 Sensitivity Mastr(20): 0.672 Pknots: 0.662 Positive Predictive Value Mastr(20): 0.790 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs Pknots Matthews Correlation Coefficient Murlet(seed): 0.451 Pknots: 0.444 Sensitivity Murlet(seed): 0.267 Pknots: 0.428 Positive Predictive Value Murlet(seed): 0.771 Pknots: 0.471 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 0.000150377120024	- RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.610 Pknots: 0.606 Sensitivity RNASLOpt: 0.566 Pknots: 0.595 Positive Predictive Value RNASLOpt: 0.665 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 8.67590017402e-07	- Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.621 Pknots: 0.614 Sensitivity Cylofold: 0.599 Pknots: 0.603 Positive Predictive Value Cylofold: 0.650 Pknots: 0.632 Number of pairs reference - predicted secondary structure: 676 Wilcoxon single-rank test P-value: 6.06606238843e-08	+ Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.606 RNAwolf: 0.550 Sensitivity Pknots: 0.595 RNAwolf: 0.554 Positive Predictive Value Pknots: 0.624 RNAwolf: 0.554 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.606 Vsfold4: 0.592 Sensitivity Pknots: 0.595 Vsfold4: 0.544 Positive Predictive Value Pknots: 0.624 Vsfold4: 0.651 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.606 Vsfold5: 0.579 Sensitivity Pknots: 0.595 Vsfold5: 0.548 Positive Predictive Value Pknots: 0.624 Vsfold5: 0.620 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.610 Alterna: 0.552 Sensitivity Pknots: 0.599 Alterna: 0.547 Positive Predictive Value Pknots: 0.629 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.610 RDfolder: 0.520 Sensitivity Pknots: 0.599 RDfolder: 0.464 Positive Predictive Value Pknots: 0.629 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(seed) vs Pknots Matthews Correlation Coefficient Carnac(seed): 0.498 Pknots: 0.484 Sensitivity Carnac(seed): 0.276 Pknots: 0.470 Positive Predictive Value Carnac(seed): 0.907 Pknots: 0.509 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 0.000186465496926	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.598 MCFold: 0.466 Sensitivity Pknots: 0.585 MCFold: 0.521 Positive Predictive Value Pknots: 0.620 MCFold: 0.426 Number of pairs reference - predicted secondary structure: 653 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.509 RSpredict(seed): 0.475 Sensitivity Pknots: 0.504 RSpredict(seed): 0.341 Positive Predictive Value Pknots: 0.523 RSpredict(seed): 0.669 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.604 NanoFolder: 0.390 Sensitivity Pknots: 0.590 NanoFolder: 0.447 Positive Predictive Value Pknots: 0.625 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.533 Mastr(seed): 0.307 Sensitivity Pknots: 0.528 Mastr(seed): 0.117 Positive Predictive Value Pknots: 0.545 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 158 Wilcoxon single-rank test P-value: 3.56938820447e-08
McQFold	51 TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.791 McQFold: 0.516 Sensitivity TurboFold(seed): 0.762 McQFold: 0.503 Positive Predictive Value TurboFold(seed): 0.822 McQFold: 0.531 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1141 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 McQFold: 0.478 Sensitivity PETfold_pre2.0(seed): 0.646 McQFold: 0.466 Positive Predictive Value PETfold_pre2.0(seed): 0.827 McQFold: 0.492 Number of pairs reference - predicted secondary structure: 1141 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.730 McQFold: 0.467 Sensitivity ContextFold: 0.696 McQFold: 0.457 Positive Predictive Value ContextFold: 0.768 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.787 McQFold: 0.484 Sensitivity TurboFold(20): 0.740 McQFold: 0.464 Positive Predictive Value TurboFold(20): 0.837 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.719 McQFold: 0.475 Sensitivity CentroidAlifold(seed): 0.571 McQFold: 0.458 Positive Predictive Value CentroidAlifold(seed): 0.905 McQFold: 0.495 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	562 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 McQFold: 0.484 Sensitivity PETfold_pre2.0(20): 0.675 McQFold: 0.464 Positive Predictive Value PETfold_pre2.0(20): 0.870 McQFold: 0.508 Number of pairs reference - predicted secondary structure: 562 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.757 McQFold: 0.484 Sensitivity CentroidAlifold(20): 0.618 McQFold: 0.464 Positive Predictive Value CentroidAlifold(20): 0.928 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 McQFold: 0.479 Sensitivity CentroidHomfold‑LAST: 0.527 McQFold: 0.466 Positive Predictive Value CentroidHomfold‑LAST: 0.850 McQFold: 0.494 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	552 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.759 McQFold: 0.484 Sensitivity PPfold(20): 0.652 McQFold: 0.464 Positive Predictive Value PPfold(20): 0.885 McQFold: 0.508 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.705 McQFold: 0.484 Sensitivity RNAalifold(20): 0.577 McQFold: 0.464 Positive Predictive Value RNAalifold(20): 0.863 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	664 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.651 McQFold: 0.478 Sensitivity MXScarna(seed): 0.556 McQFold: 0.460 Positive Predictive Value MXScarna(seed): 0.764 McQFold: 0.498 Number of pairs reference - predicted secondary structure: 664 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.701 McQFold: 0.484 Sensitivity MXScarna(20): 0.634 McQFold: 0.464 Positive Predictive Value MXScarna(20): 0.776 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.626 McQFold: 0.467 Sensitivity IPknot: 0.577 McQFold: 0.457 Positive Predictive Value IPknot: 0.679 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.685 McQFold: 0.485 Sensitivity Multilign(20): 0.617 McQFold: 0.465 Positive Predictive Value Multilign(20): 0.762 McQFold: 0.509 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	495 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.631 McQFold: 0.485 Sensitivity Murlet(20): 0.496 McQFold: 0.466 Positive Predictive Value Murlet(20): 0.803 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	632 RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.548 McQFold: 0.474 Sensitivity RNAalifold(seed): 0.350 McQFold: 0.456 Positive Predictive Value RNAalifold(seed): 0.859 McQFold: 0.494 Number of pairs reference - predicted secondary structure: 632 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.593 McQFold: 0.467 Sensitivity CentroidFold: 0.546 McQFold: 0.457 Positive Predictive Value CentroidFold: 0.646 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.676 McQFold: 0.504 Sensitivity RNASampler(20): 0.522 McQFold: 0.487 Positive Predictive Value RNASampler(20): 0.877 McQFold: 0.525 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.580 McQFold: 0.467 Sensitivity Contrafold: 0.570 McQFold: 0.457 Positive Predictive Value Contrafold: 0.592 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.552 McQFold: 0.467 Sensitivity Sfold: 0.507 McQFold: 0.457 Positive Predictive Value Sfold: 0.602 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs McQFold Matthews Correlation Coefficient Multilign(seed): 0.681 McQFold: 0.509 Sensitivity Multilign(seed): 0.649 McQFold: 0.509 Positive Predictive Value Multilign(seed): 0.717 McQFold: 0.512 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	1707 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.553 McQFold: 0.467 Sensitivity MaxExpect: 0.542 McQFold: 0.457 Positive Predictive Value MaxExpect: 0.565 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.550 McQFold: 0.467 Sensitivity ProbKnot: 0.548 McQFold: 0.457 Positive Predictive Value ProbKnot: 0.553 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.531 McQFold: 0.467 Sensitivity Fold: 0.535 McQFold: 0.457 Positive Predictive Value Fold: 0.529 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.629 McQFold: 0.524 Sensitivity RNASampler(seed): 0.468 McQFold: 0.496 Positive Predictive Value RNASampler(seed): 0.847 McQFold: 0.557 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.522 McQFold: 0.467 Sensitivity UNAFold: 0.519 McQFold: 0.457 Positive Predictive Value UNAFold: 0.526 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.525 McQFold: 0.479 Sensitivity RNAsubopt: 0.530 McQFold: 0.466 Positive Predictive Value RNAsubopt: 0.521 McQFold: 0.494 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.524 McQFold: 0.484 Sensitivity RSpredict(20): 0.385 McQFold: 0.464 Positive Predictive Value RSpredict(20): 0.714 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.549 McQFold: 0.483 Sensitivity CMfinder(20): 0.380 McQFold: 0.463 Positive Predictive Value CMfinder(20): 0.794 McQFold: 0.507 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.520 McQFold: 0.467 Sensitivity PknotsRG: 0.522 McQFold: 0.457 Positive Predictive Value PknotsRG: 0.518 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 McQFold vs Carnac(20) Matthews Correlation Coefficient McQFold: 0.484 Carnac(20): 0.469 Sensitivity McQFold: 0.464 Carnac(20): 0.248 Positive Predictive Value McQFold: 0.507 Carnac(20): 0.888 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.518 McQFold: 0.467 Sensitivity RNAfold: 0.521 McQFold: 0.457 Positive Predictive Value RNAfold: 0.517 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: 0.502 CMfinder(seed): 0.486 Sensitivity McQFold: 0.485 CMfinder(seed): 0.312 Positive Predictive Value McQFold: 0.520 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 1.70738736246e-07	1061 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.519 McQFold: 0.460 Sensitivity Afold: 0.517 McQFold: 0.447 Positive Predictive Value Afold: 0.523 McQFold: 0.475 Number of pairs reference - predicted secondary structure: 1061 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.613 McQFold: 0.583 Sensitivity HotKnots: 0.607 McQFold: 0.557 Positive Predictive Value HotKnots: 0.624 McQFold: 0.615 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	1706 CRWrnafold vs McQFold Matthews Correlation Coefficient CRWrnafold: 0.468 McQFold: 0.467 Sensitivity CRWrnafold: 0.471 McQFold: 0.457 Positive Predictive Value CRWrnafold: 0.466 McQFold: 0.480 Number of pairs reference - predicted secondary structure: 1706 Wilcoxon single-rank test P-value: 0.0853441262641	697 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.650 Pknots: 0.606 Sensitivity McQFold: 0.621 Pknots: 0.595 Positive Predictive Value McQFold: 0.686 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.481 RNAshapes: 0.477 Sensitivity McQFold: 0.468 RNAshapes: 0.472 Positive Predictive Value McQFold: 0.497 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs McQFold Matthews Correlation Coefficient PPfold(seed): 0.626 McQFold: 0.532 Sensitivity PPfold(seed): 0.495 McQFold: 0.521 Positive Predictive Value PPfold(seed): 0.794 McQFold: 0.546 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.484 Mastr(20): 0.350 Sensitivity McQFold: 0.464 Mastr(20): 0.156 Positive Predictive Value McQFold: 0.507 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs McQFold Matthews Correlation Coefficient Murlet(seed): 0.530 McQFold: 0.500 Sensitivity Murlet(seed): 0.336 McQFold: 0.480 Positive Predictive Value Murlet(seed): 0.839 McQFold: 0.523 Number of pairs reference - predicted secondary structure: 122 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.480 RNASLOpt: 0.470 Sensitivity McQFold: 0.467 RNASLOpt: 0.442 Positive Predictive Value McQFold: 0.497 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.616 Cylofold: 0.575 Sensitivity McQFold: 0.587 Cylofold: 0.551 Positive Predictive Value McQFold: 0.653 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.467 RNAwolf: 0.371 Sensitivity McQFold: 0.457 RNAwolf: 0.386 Positive Predictive Value McQFold: 0.480 RNAwolf: 0.358 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.480 Vsfold4: 0.346 Sensitivity McQFold: 0.467 Vsfold4: 0.318 Positive Predictive Value McQFold: 0.495 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.481 Vsfold5: 0.339 Sensitivity McQFold: 0.467 Vsfold5: 0.322 Positive Predictive Value McQFold: 0.496 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.653 Alterna: 0.552 Sensitivity McQFold: 0.624 Alterna: 0.547 Positive Predictive Value McQFold: 0.689 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.653 RDfolder: 0.520 Sensitivity McQFold: 0.624 RDfolder: 0.464 Positive Predictive Value McQFold: 0.689 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.454 Carnac(seed): 0.215 Sensitivity McQFold: 0.444 Carnac(seed): 0.055 Positive Predictive Value McQFold: 0.467 Carnac(seed): 0.850 Number of pairs reference - predicted secondary structure: 268 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.593 MCFold: 0.473 Sensitivity McQFold: 0.563 MCFold: 0.524 Positive Predictive Value McQFold: 0.631 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.475 RSpredict(seed): 0.237 Sensitivity McQFold: 0.458 RSpredict(seed): 0.107 Positive Predictive Value McQFold: 0.495 RSpredict(seed): 0.528 Number of pairs reference - predicted secondary structure: 645 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.479 NanoFolder: 0.194 Sensitivity McQFold: 0.464 NanoFolder: 0.229 Positive Predictive Value McQFold: 0.496 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.479 Mastr(seed): 0.115 Sensitivity McQFold: 0.462 Mastr(seed): 0.016 Positive Predictive Value McQFold: 0.498 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAshapes	49 TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.782 RNAshapes: 0.643 Sensitivity TurboFold(seed): 0.756 RNAshapes: 0.647 Positive Predictive Value TurboFold(seed): 0.811 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	1095 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.737 RNAshapes: 0.465 Sensitivity PETfold_pre2.0(seed): 0.657 RNAshapes: 0.462 Positive Predictive Value PETfold_pre2.0(seed): 0.828 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 1095 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.753 RNAshapes: 0.477 Sensitivity ContextFold: 0.715 RNAshapes: 0.472 Positive Predictive Value ContextFold: 0.794 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	555 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.787 RNAshapes: 0.526 Sensitivity TurboFold(20): 0.741 RNAshapes: 0.514 Positive Predictive Value TurboFold(20): 0.838 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	604 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.726 RNAshapes: 0.528 Sensitivity CentroidAlifold(seed): 0.583 RNAshapes: 0.517 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 604 Wilcoxon single-rank test P-value: 3.56938820447e-08	552 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.768 RNAshapes: 0.526 Sensitivity PETfold_pre2.0(20): 0.677 RNAshapes: 0.513 Positive Predictive Value PETfold_pre2.0(20): 0.873 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	555 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.759 RNAshapes: 0.526 Sensitivity CentroidAlifold(20): 0.620 RNAshapes: 0.514 Positive Predictive Value CentroidAlifold(20): 0.929 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.673 RNAshapes: 0.477 Sensitivity CentroidHomfold‑LAST: 0.534 RNAshapes: 0.472 Positive Predictive Value CentroidHomfold‑LAST: 0.850 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	543 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.762 RNAshapes: 0.526 Sensitivity PPfold(20): 0.655 RNAshapes: 0.513 Positive Predictive Value PPfold(20): 0.889 RNAshapes: 0.540 Number of pairs reference - predicted secondary structure: 543 Wilcoxon single-rank test P-value: 3.56938820447e-08	555 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.708 RNAshapes: 0.526 Sensitivity RNAalifold(20): 0.580 RNAshapes: 0.514 Positive Predictive Value RNAalifold(20): 0.867 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	626 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.662 RNAshapes: 0.527 Sensitivity MXScarna(seed): 0.570 RNAshapes: 0.516 Positive Predictive Value MXScarna(seed): 0.771 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	555 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.701 RNAshapes: 0.526 Sensitivity MXScarna(20): 0.635 RNAshapes: 0.514 Positive Predictive Value MXScarna(20): 0.776 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.637 RNAshapes: 0.477 Sensitivity IPknot: 0.589 RNAshapes: 0.472 Positive Predictive Value IPknot: 0.691 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	525 Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.687 RNAshapes: 0.526 Sensitivity Multilign(20): 0.619 RNAshapes: 0.514 Positive Predictive Value Multilign(20): 0.763 RNAshapes: 0.540 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	489 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.636 RNAshapes: 0.526 Sensitivity Murlet(20): 0.501 RNAshapes: 0.515 Positive Predictive Value Murlet(20): 0.808 RNAshapes: 0.539 Number of pairs reference - predicted secondary structure: 489 Wilcoxon single-rank test P-value: 3.56938820447e-08	594 RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.549 RNAshapes: 0.527 Sensitivity RNAalifold(seed): 0.351 RNAshapes: 0.516 Positive Predictive Value RNAalifold(seed): 0.858 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 594 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.601 RNAshapes: 0.477 Sensitivity CentroidFold: 0.554 RNAshapes: 0.472 Positive Predictive Value CentroidFold: 0.653 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	392 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.677 RNAshapes: 0.560 Sensitivity RNASampler(20): 0.522 RNAshapes: 0.556 Positive Predictive Value RNASampler(20): 0.879 RNAshapes: 0.566 Number of pairs reference - predicted secondary structure: 392 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.588 RNAshapes: 0.477 Sensitivity Contrafold: 0.577 RNAshapes: 0.472 Positive Predictive Value Contrafold: 0.600 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.562 RNAshapes: 0.477 Sensitivity Sfold: 0.516 RNAshapes: 0.472 Positive Predictive Value Sfold: 0.615 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.665 RNAshapes: 0.491 Sensitivity Multilign(seed): 0.632 RNAshapes: 0.502 Positive Predictive Value Multilign(seed): 0.701 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	1588 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.565 RNAshapes: 0.477 Sensitivity MaxExpect: 0.552 RNAshapes: 0.472 Positive Predictive Value MaxExpect: 0.579 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.563 RNAshapes: 0.477 Sensitivity ProbKnot: 0.558 RNAshapes: 0.472 Positive Predictive Value ProbKnot: 0.570 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.546 RNAshapes: 0.477 Sensitivity Fold: 0.547 RNAshapes: 0.472 Positive Predictive Value Fold: 0.547 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	97 RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.623 RNAshapes: 0.555 Sensitivity RNASampler(seed): 0.461 RNAshapes: 0.544 Positive Predictive Value RNASampler(seed): 0.844 RNAshapes: 0.569 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.534 RNAshapes: 0.477 Sensitivity UNAFold: 0.528 RNAshapes: 0.472 Positive Predictive Value UNAFold: 0.541 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.526 RNAshapes: 0.477 Sensitivity RNAsubopt: 0.531 RNAshapes: 0.472 Positive Predictive Value RNAsubopt: 0.523 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	555 RSpredict(20) vs RNAshapes Matthews Correlation Coefficient RSpredict(20): 0.533 RNAshapes: 0.526 Sensitivity RSpredict(20): 0.394 RNAshapes: 0.514 Positive Predictive Value RSpredict(20): 0.721 RNAshapes: 0.541 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 4.48494289621e-08	551 CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.557 RNAshapes: 0.525 Sensitivity CMfinder(20): 0.388 RNAshapes: 0.513 Positive Predictive Value CMfinder(20): 0.800 RNAshapes: 0.540 Number of pairs reference - predicted secondary structure: 551 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.531 RNAshapes: 0.477 Sensitivity PknotsRG: 0.530 RNAshapes: 0.472 Positive Predictive Value PknotsRG: 0.533 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	555 RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.526 Carnac(20): 0.472 Sensitivity RNAshapes: 0.514 Carnac(20): 0.251 Positive Predictive Value RNAshapes: 0.541 Carnac(20): 0.890 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.533 RNAshapes: 0.477 Sensitivity RNAfold: 0.532 RNAshapes: 0.472 Positive Predictive Value RNAfold: 0.535 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 RNAshapes vs CMfinder(seed) Matthews Correlation Coefficient RNAshapes: 0.555 CMfinder(seed): 0.489 Sensitivity RNAshapes: 0.548 CMfinder(seed): 0.316 Positive Predictive Value RNAshapes: 0.564 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	967 Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.539 RNAshapes: 0.514 Sensitivity Afold: 0.532 RNAshapes: 0.504 Positive Predictive Value Afold: 0.548 RNAshapes: 0.528 Number of pairs reference - predicted secondary structure: 967 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.613 RNAshapes: 0.612 Sensitivity HotKnots: 0.607 RNAshapes: 0.603 Positive Predictive Value HotKnots: 0.624 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 0.581569793731	1587 CRWrnafold vs RNAshapes Matthews Correlation Coefficient CRWrnafold: 0.484 RNAshapes: 0.477 Sensitivity CRWrnafold: 0.483 RNAshapes: 0.472 Positive Predictive Value CRWrnafold: 0.486 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1587 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: 0.606 RNAshapes: 0.594 Sensitivity Pknots: 0.595 RNAshapes: 0.585 Positive Predictive Value Pknots: 0.624 RNAshapes: 0.610 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.481 RNAshapes: 0.477 Sensitivity McQFold: 0.468 RNAshapes: 0.472 Positive Predictive Value McQFold: 0.497 RNAshapes: 0.484 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.633 PPfold(seed): 0.624 Sensitivity RNAshapes: 0.639 PPfold(seed): 0.499 Positive Predictive Value RNAshapes: 0.629 PPfold(seed): 0.782 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 0.000349712763079	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.526 Mastr(20): 0.357 Sensitivity RNAshapes: 0.514 Mastr(20): 0.162 Positive Predictive Value RNAshapes: 0.541 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.564 Murlet(seed): 0.511 Sensitivity RNAshapes: 0.559 Murlet(seed): 0.315 Positive Predictive Value RNAshapes: 0.571 Murlet(seed): 0.833 Number of pairs reference - predicted secondary structure: 119 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.480 RNASLOpt: 0.471 Sensitivity RNAshapes: 0.475 RNASLOpt: 0.444 Positive Predictive Value RNAshapes: 0.486 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1533 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.632 Cylofold: 0.575 Sensitivity RNAshapes: 0.621 Cylofold: 0.551 Positive Predictive Value RNAshapes: 0.649 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.477 RNAwolf: 0.388 Sensitivity RNAshapes: 0.472 RNAwolf: 0.402 Positive Predictive Value RNAshapes: 0.484 RNAwolf: 0.378 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.476 Vsfold4: 0.349 Sensitivity RNAshapes: 0.472 Vsfold4: 0.321 Positive Predictive Value RNAshapes: 0.483 Vsfold4: 0.382 Number of pairs reference - predicted secondary structure: 1584 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.476 Vsfold5: 0.341 Sensitivity RNAshapes: 0.471 Vsfold5: 0.324 Positive Predictive Value RNAshapes: 0.483 Vsfold5: 0.361 Number of pairs reference - predicted secondary structure: 1583 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.596 Alterna: 0.552 Sensitivity RNAshapes: 0.587 Alterna: 0.547 Positive Predictive Value RNAshapes: 0.612 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.596 RDfolder: 0.520 Sensitivity RNAshapes: 0.587 RDfolder: 0.464 Positive Predictive Value RNAshapes: 0.612 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.544 Carnac(seed): 0.228 Sensitivity RNAshapes: 0.539 Carnac(seed): 0.059 Positive Predictive Value RNAshapes: 0.551 Carnac(seed): 0.881 Number of pairs reference - predicted secondary structure: 241 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.617 MCFold: 0.473 Sensitivity RNAshapes: 0.605 MCFold: 0.524 Positive Predictive Value RNAshapes: 0.635 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.527 RSpredict(seed): 0.240 Sensitivity RNAshapes: 0.516 RSpredict(seed): 0.109 Positive Predictive Value RNAshapes: 0.540 RSpredict(seed): 0.533 Number of pairs reference - predicted secondary structure: 607 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.491 NanoFolder: 0.200 Sensitivity RNAshapes: 0.482 NanoFolder: 0.235 Positive Predictive Value RNAshapes: 0.502 NanoFolder: 0.173 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.528 Mastr(seed): 0.115 Sensitivity RNAshapes: 0.518 Mastr(seed): 0.016 Positive Predictive Value RNAshapes: 0.540 Mastr(seed): 0.812 Number of pairs reference - predicted secondary structure: 605 Wilcoxon single-rank test P-value: 3.56938820447e-08
PPfold(seed)	40 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.789 PPfold(seed): 0.687 Sensitivity TurboFold(seed): 0.755 PPfold(seed): 0.565 Positive Predictive Value TurboFold(seed): 0.826 PPfold(seed): 0.836 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.747 PPfold(seed): 0.629 Sensitivity PETfold_pre2.0(seed): 0.693 PPfold(seed): 0.500 Positive Predictive Value PETfold_pre2.0(seed): 0.806 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.773 PPfold(seed): 0.626 Sensitivity ContextFold: 0.755 PPfold(seed): 0.495 Positive Predictive Value ContextFold: 0.793 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.872 PPfold(seed): 0.453 Sensitivity TurboFold(20): 0.866 PPfold(seed): 0.224 Positive Predictive Value TurboFold(20): 0.880 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.02343278931e-08	63 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 PPfold(seed): 0.626 Sensitivity CentroidAlifold(seed): 0.646 PPfold(seed): 0.495 Positive Predictive Value CentroidAlifold(seed): 0.832 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.669 PPfold(seed): 0.453 Sensitivity PETfold_pre2.0(20): 0.473 PPfold(seed): 0.224 Positive Predictive Value PETfold_pre2.0(20): 0.948 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.69811216434e-08	24 CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.736 PPfold(seed): 0.453 Sensitivity CentroidAlifold(20): 0.576 PPfold(seed): 0.224 Positive Predictive Value CentroidAlifold(20): 0.943 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	62 CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 PPfold(seed): 0.635 Sensitivity CentroidHomfold‑LAST: 0.676 PPfold(seed): 0.511 Positive Predictive Value CentroidHomfold‑LAST: 0.830 PPfold(seed): 0.790 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.640 PPfold(seed): 0.453 Sensitivity PPfold(20): 0.434 PPfold(seed): 0.224 Positive Predictive Value PPfold(20): 0.947 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	24 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.704 PPfold(seed): 0.453 Sensitivity RNAalifold(20): 0.524 PPfold(seed): 0.224 Positive Predictive Value RNAalifold(20): 0.948 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.85839946686e-08	63 MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.720 PPfold(seed): 0.626 Sensitivity MXScarna(seed): 0.692 PPfold(seed): 0.495 Positive Predictive Value MXScarna(seed): 0.751 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.838 PPfold(seed): 0.453 Sensitivity MXScarna(20): 0.778 PPfold(seed): 0.224 Positive Predictive Value MXScarna(20): 0.904 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.89920829651e-08	63 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.725 PPfold(seed): 0.626 Sensitivity IPknot: 0.708 PPfold(seed): 0.495 Positive Predictive Value IPknot: 0.744 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.611 PPfold(seed): 0.354 Sensitivity Multilign(20): 0.462 PPfold(seed): 0.136 Positive Predictive Value Multilign(20): 0.811 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	23 Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.646 PPfold(seed): 0.463 Sensitivity Murlet(20): 0.453 PPfold(seed): 0.233 Positive Predictive Value Murlet(20): 0.923 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	54 RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.669 PPfold(seed): 0.648 Sensitivity RNAalifold(seed): 0.521 PPfold(seed): 0.530 Positive Predictive Value RNAalifold(seed): 0.860 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.679 PPfold(seed): 0.626 Sensitivity CentroidFold: 0.654 PPfold(seed): 0.495 Positive Predictive Value CentroidFold: 0.707 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.620 PPfold(seed): 0.453 Sensitivity RNASampler(20): 0.407 PPfold(seed): 0.224 Positive Predictive Value RNASampler(20): 0.949 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	63 Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.676 PPfold(seed): 0.626 Sensitivity Contrafold: 0.676 PPfold(seed): 0.495 Positive Predictive Value Contrafold: 0.677 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.682 PPfold(seed): 0.626 Sensitivity Sfold: 0.657 PPfold(seed): 0.495 Positive Predictive Value Sfold: 0.709 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): 0.751 Multilign(seed): 0.698 Sensitivity PPfold(seed): 0.675 Multilign(seed): 0.660 Positive Predictive Value PPfold(seed): 0.838 Multilign(seed): 0.741 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	63 MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.665 PPfold(seed): 0.626 Sensitivity MaxExpect: 0.670 PPfold(seed): 0.495 Positive Predictive Value MaxExpect: 0.662 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.667 PPfold(seed): 0.626 Sensitivity ProbKnot: 0.679 PPfold(seed): 0.495 Positive Predictive Value ProbKnot: 0.656 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.657 PPfold(seed): 0.626 Sensitivity Fold: 0.667 PPfold(seed): 0.495 Positive Predictive Value Fold: 0.648 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 PPfold(seed) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(seed): 0.862 RNASampler(seed): 0.713 Sensitivity PPfold(seed): 0.777 RNASampler(seed): 0.571 Positive Predictive Value PPfold(seed): 0.957 RNASampler(seed): 0.890 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	63 UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.653 PPfold(seed): 0.626 Sensitivity UNAFold: 0.657 PPfold(seed): 0.495 Positive Predictive Value UNAFold: 0.651 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.668 PPfold(seed): 0.635 Sensitivity RNAsubopt: 0.679 PPfold(seed): 0.511 Positive Predictive Value RNAsubopt: 0.660 PPfold(seed): 0.790 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.784 PPfold(seed): 0.453 Sensitivity RSpredict(20): 0.671 PPfold(seed): 0.224 Positive Predictive Value RSpredict(20): 0.917 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	24 CMfinder(20) vs PPfold(seed) Matthews Correlation Coefficient CMfinder(20): 0.711 PPfold(seed): 0.453 Sensitivity CMfinder(20): 0.563 PPfold(seed): 0.224 Positive Predictive Value CMfinder(20): 0.901 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	63 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.678 PPfold(seed): 0.626 Sensitivity PknotsRG: 0.688 PPfold(seed): 0.495 Positive Predictive Value PknotsRG: 0.670 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.487 PPfold(seed): 0.453 Sensitivity Carnac(20): 0.277 PPfold(seed): 0.224 Positive Predictive Value Carnac(20): 0.861 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 6.32937386918e-08	63 RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.678 PPfold(seed): 0.626 Sensitivity RNAfold: 0.685 PPfold(seed): 0.495 Positive Predictive Value RNAfold: 0.672 PPfold(seed): 0.794 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): 0.861 CMfinder(seed): 0.566 Sensitivity PPfold(seed): 0.774 CMfinder(seed): 0.427 Positive Predictive Value PPfold(seed): 0.959 CMfinder(seed): 0.752 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.98172311752e-08	42 PPfold(seed) vs Afold Matthews Correlation Coefficient PPfold(seed): 0.685 Afold: 0.638 Sensitivity PPfold(seed): 0.581 Afold: 0.642 Positive Predictive Value PPfold(seed): 0.808 Afold: 0.636 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.702 PPfold(seed): 0.380 Sensitivity HotKnots: 0.713 PPfold(seed): 0.170 Positive Predictive Value HotKnots: 0.697 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 PPfold(seed) vs CRWrnafold Matthews Correlation Coefficient PPfold(seed): 0.626 CRWrnafold: 0.565 Sensitivity PPfold(seed): 0.495 CRWrnafold: 0.572 Positive Predictive Value PPfold(seed): 0.794 CRWrnafold: 0.559 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.646 PPfold(seed): 0.488 Sensitivity Pknots: 0.645 PPfold(seed): 0.281 Positive Predictive Value Pknots: 0.653 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 PPfold(seed) vs McQFold Matthews Correlation Coefficient PPfold(seed): 0.626 McQFold: 0.532 Sensitivity PPfold(seed): 0.495 McQFold: 0.521 Positive Predictive Value PPfold(seed): 0.794 McQFold: 0.546 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.633 PPfold(seed): 0.624 Sensitivity RNAshapes: 0.639 PPfold(seed): 0.499 Positive Predictive Value RNAshapes: 0.629 PPfold(seed): 0.782 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 0.000349712763079		- Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.665 PPfold(seed): 0.453 Sensitivity Mastr(20): 0.492 PPfold(seed): 0.224 Positive Predictive Value Mastr(20): 0.902 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PPfold(seed) vs Murlet(seed) Matthews Correlation Coefficient PPfold(seed): 0.742 Murlet(seed): 0.588 Sensitivity PPfold(seed): 0.657 Murlet(seed): 0.411 Positive Predictive Value PPfold(seed): 0.839 Murlet(seed): 0.842 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(seed) vs RNASLOpt Matthews Correlation Coefficient PPfold(seed): 0.635 RNASLOpt: 0.542 Sensitivity PPfold(seed): 0.511 RNASLOpt: 0.516 Positive Predictive Value PPfold(seed): 0.790 RNASLOpt: 0.572 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.624 PPfold(seed): 0.375 Sensitivity Cylofold: 0.593 PPfold(seed): 0.167 Positive Predictive Value Cylofold: 0.661 PPfold(seed): 0.845 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(seed) vs RNAwolf Matthews Correlation Coefficient PPfold(seed): 0.626 RNAwolf: 0.461 Sensitivity PPfold(seed): 0.495 RNAwolf: 0.477 Positive Predictive Value PPfold(seed): 0.794 RNAwolf: 0.448 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): 0.635 Vsfold4: 0.244 Sensitivity PPfold(seed): 0.511 Vsfold4: 0.225 Positive Predictive Value PPfold(seed): 0.790 Vsfold4: 0.268 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(seed) vs Vsfold5 Matthews Correlation Coefficient PPfold(seed): 0.635 Vsfold5: 0.233 Sensitivity PPfold(seed): 0.511 Vsfold5: 0.221 Positive Predictive Value PPfold(seed): 0.790 Vsfold5: 0.250 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.543 PPfold(seed): 0.501 Sensitivity Alterna: 0.529 PPfold(seed): 0.297 Positive Predictive Value Alterna: 0.565 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	- RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.528 PPfold(seed): 0.501 Sensitivity RDfolder: 0.462 PPfold(seed): 0.297 Positive Predictive Value RDfolder: 0.612 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.16498238667e-07	+ PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.631 Carnac(seed): 0.369 Sensitivity PPfold(seed): 0.502 Carnac(seed): 0.153 Positive Predictive Value PPfold(seed): 0.794 Carnac(seed): 0.896 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.421 PPfold(seed): 0.417 Sensitivity MCFold: 0.478 PPfold(seed): 0.206 Positive Predictive Value MCFold: 0.378 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 0.135703339508	+ PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.626 RSpredict(seed): 0.398 Sensitivity PPfold(seed): 0.495 RSpredict(seed): 0.277 Positive Predictive Value PPfold(seed): 0.794 RSpredict(seed): 0.574 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(seed) vs NanoFolder Matthews Correlation Coefficient PPfold(seed): 0.599 NanoFolder: 0.368 Sensitivity PPfold(seed): 0.383 NanoFolder: 0.429 Positive Predictive Value PPfold(seed): 0.939 NanoFolder: 0.322 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.74569091494e-09	+ PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.626 Mastr(seed): 0.324 Sensitivity PPfold(seed): 0.495 Mastr(seed): 0.125 Positive Predictive Value PPfold(seed): 0.794 Mastr(seed): 0.845 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08
Mastr(20)	19 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.858 Mastr(20): 0.653 Sensitivity TurboFold(seed): 0.851 Mastr(20): 0.460 Positive Predictive Value TurboFold(seed): 0.867 Mastr(20): 0.931 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.39090039918e-08	576 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.752 Mastr(20): 0.301 Sensitivity PETfold_pre2.0(seed): 0.694 Mastr(20): 0.114 Positive Predictive Value PETfold_pre2.0(seed): 0.817 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 576 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.748 Mastr(20): 0.296 Sensitivity ContextFold: 0.712 Mastr(20): 0.111 Positive Predictive Value ContextFold: 0.787 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.787 Mastr(20): 0.350 Sensitivity TurboFold(20): 0.740 Mastr(20): 0.156 Positive Predictive Value TurboFold(20): 0.837 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	353 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.716 Mastr(20): 0.224 Sensitivity CentroidAlifold(seed): 0.558 Mastr(20): 0.061 Positive Predictive Value CentroidAlifold(seed): 0.921 Mastr(20): 0.827 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	589 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.707 Mastr(20): 0.297 Sensitivity PETfold_pre2.0(20): 0.634 Mastr(20): 0.111 Positive Predictive Value PETfold_pre2.0(20): 0.788 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 589 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.694 Mastr(20): 0.296 Sensitivity CentroidAlifold(20): 0.550 Mastr(20): 0.111 Positive Predictive Value CentroidAlifold(20): 0.877 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.749 Mastr(20): 0.350 Sensitivity CentroidHomfold‑LAST: 0.625 Mastr(20): 0.156 Positive Predictive Value CentroidHomfold‑LAST: 0.899 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	554 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.754 Mastr(20): 0.349 Sensitivity PPfold(20): 0.648 Mastr(20): 0.154 Positive Predictive Value PPfold(20): 0.879 Mastr(20): 0.792 Number of pairs reference - predicted secondary structure: 554 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.625 Mastr(20): 0.296 Sensitivity RNAalifold(20): 0.523 Mastr(20): 0.111 Positive Predictive Value RNAalifold(20): 0.747 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	367 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.665 Mastr(20): 0.239 Sensitivity MXScarna(seed): 0.582 Mastr(20): 0.069 Positive Predictive Value MXScarna(seed): 0.760 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 367 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.629 Mastr(20): 0.296 Sensitivity MXScarna(20): 0.574 Mastr(20): 0.111 Positive Predictive Value MXScarna(20): 0.690 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.604 Mastr(20): 0.296 Sensitivity IPknot: 0.546 Mastr(20): 0.111 Positive Predictive Value IPknot: 0.668 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.685 Mastr(20): 0.360 Sensitivity Multilign(20): 0.617 Mastr(20): 0.165 Positive Predictive Value Multilign(20): 0.762 Mastr(20): 0.788 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	497 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.620 Mastr(20): 0.389 Sensitivity Murlet(20): 0.488 Mastr(20): 0.191 Positive Predictive Value Murlet(20): 0.789 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 497 Wilcoxon single-rank test P-value: 3.56938820447e-08	352 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.490 Mastr(20): 0.213 Sensitivity RNAalifold(seed): 0.318 Mastr(20): 0.055 Positive Predictive Value RNAalifold(seed): 0.755 Mastr(20): 0.822 Number of pairs reference - predicted secondary structure: 352 Wilcoxon single-rank test P-value: 3.56938820447e-08	591 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.578 Mastr(20): 0.298 Sensitivity CentroidFold: 0.523 Mastr(20): 0.112 Positive Predictive Value CentroidFold: 0.640 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 591 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.676 Mastr(20): 0.510 Sensitivity RNASampler(20): 0.522 Mastr(20): 0.331 Positive Predictive Value RNASampler(20): 0.877 Mastr(20): 0.789 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.561 Mastr(20): 0.296 Sensitivity Contrafold: 0.547 Mastr(20): 0.111 Positive Predictive Value Contrafold: 0.577 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.534 Mastr(20): 0.296 Sensitivity Sfold: 0.482 Mastr(20): 0.111 Positive Predictive Value Sfold: 0.593 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 Mastr(20) vs Multilign(seed) Matthews Correlation Coefficient Mastr(20): 0.775 Multilign(seed): 0.334 Sensitivity Mastr(20): 0.721 Multilign(seed): 0.186 Positive Predictive Value Mastr(20): 0.838 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	592 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.533 Mastr(20): 0.296 Sensitivity MaxExpect: 0.521 Mastr(20): 0.111 Positive Predictive Value MaxExpect: 0.547 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.529 Mastr(20): 0.296 Sensitivity ProbKnot: 0.522 Mastr(20): 0.111 Positive Predictive Value ProbKnot: 0.536 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.510 Mastr(20): 0.296 Sensitivity Fold: 0.512 Mastr(20): 0.111 Positive Predictive Value Fold: 0.509 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Mastr(20) vs RNASampler(seed) Matthews Correlation Coefficient Mastr(20): 0.773 RNASampler(seed): 0.571 Sensitivity Mastr(20): 0.712 RNASampler(seed): 0.343 Positive Predictive Value Mastr(20): 0.843 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.500 Mastr(20): 0.296 Sensitivity UNAFold: 0.496 Mastr(20): 0.111 Positive Predictive Value UNAFold: 0.505 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.570 Mastr(20): 0.350 Sensitivity RNAsubopt: 0.570 Mastr(20): 0.156 Positive Predictive Value RNAsubopt: 0.573 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.387 Mastr(20): 0.296 Sensitivity RSpredict(20): 0.305 Mastr(20): 0.111 Positive Predictive Value RSpredict(20): 0.494 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.549 Mastr(20): 0.350 Sensitivity CMfinder(20): 0.380 Mastr(20): 0.155 Positive Predictive Value CMfinder(20): 0.794 Mastr(20): 0.789 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	566 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.563 Mastr(20): 0.348 Sensitivity PknotsRG: 0.556 Mastr(20): 0.154 Positive Predictive Value PknotsRG: 0.571 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 566 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.462 Mastr(20): 0.296 Sensitivity Carnac(20): 0.246 Mastr(20): 0.111 Positive Predictive Value Carnac(20): 0.869 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	592 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.497 Mastr(20): 0.296 Sensitivity RNAfold: 0.497 Mastr(20): 0.111 Positive Predictive Value RNAfold: 0.498 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 592 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): 0.748 CMfinder(seed): 0.736 Sensitivity Mastr(20): 0.683 CMfinder(seed): 0.607 Positive Predictive Value Mastr(20): 0.824 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 1.47584956762e-07	373 Afold vs Mastr(20) Matthews Correlation Coefficient Afold: 0.477 Mastr(20): 0.236 Sensitivity Afold: 0.474 Mastr(20): 0.071 Positive Predictive Value Afold: 0.480 Mastr(20): 0.782 Number of pairs reference - predicted secondary structure: 373 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs HotKnots Matthews Correlation Coefficient Mastr(20): 0.708 HotKnots: 0.698 Sensitivity Mastr(20): 0.635 HotKnots: 0.695 Positive Predictive Value Mastr(20): 0.793 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 2.12176083234e-07	566 CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.538 Mastr(20): 0.348 Sensitivity CRWrnafold: 0.529 Mastr(20): 0.154 Positive Predictive Value CRWrnafold: 0.549 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 566 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.727 Pknots: 0.655 Sensitivity Mastr(20): 0.672 Pknots: 0.662 Positive Predictive Value Mastr(20): 0.790 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.484 Mastr(20): 0.350 Sensitivity McQFold: 0.464 Mastr(20): 0.156 Positive Predictive Value McQFold: 0.507 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	555 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.526 Mastr(20): 0.357 Sensitivity RNAshapes: 0.514 Mastr(20): 0.162 Positive Predictive Value RNAshapes: 0.541 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 555 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.665 PPfold(seed): 0.453 Sensitivity Mastr(20): 0.492 PPfold(seed): 0.224 Positive Predictive Value Mastr(20): 0.902 PPfold(seed): 0.923 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08		+ Mastr(20) vs Murlet(seed) Matthews Correlation Coefficient Mastr(20): 0.697 Murlet(seed): 0.631 Sensitivity Mastr(20): 0.584 Murlet(seed): 0.418 Positive Predictive Value Mastr(20): 0.837 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.500 Mastr(20): 0.364 Sensitivity RNASLOpt: 0.464 Mastr(20): 0.168 Positive Predictive Value RNASLOpt: 0.542 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Cylofold Matthews Correlation Coefficient Mastr(20): 0.713 Cylofold: 0.557 Sensitivity Mastr(20): 0.641 Cylofold: 0.543 Positive Predictive Value Mastr(20): 0.796 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAwolf vs Mastr(20) Matthews Correlation Coefficient RNAwolf: 0.414 Mastr(20): 0.350 Sensitivity RNAwolf: 0.423 Mastr(20): 0.156 Positive Predictive Value RNAwolf: 0.408 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.390 Mastr(20): 0.354 Sensitivity Vsfold4: 0.356 Mastr(20): 0.159 Positive Predictive Value Vsfold4: 0.431 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Vsfold5 vs Mastr(20) Matthews Correlation Coefficient Vsfold5: 0.365 Mastr(20): 0.356 Sensitivity Vsfold5: 0.341 Mastr(20): 0.161 Positive Predictive Value Vsfold5: 0.394 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.730 Alterna: 0.618 Sensitivity Mastr(20): 0.677 Alterna: 0.626 Positive Predictive Value Mastr(20): 0.790 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.730 RDfolder: 0.556 Sensitivity Mastr(20): 0.677 RDfolder: 0.511 Positive Predictive Value Mastr(20): 0.790 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.532 Carnac(seed): 0.310 Sensitivity Mastr(20): 0.327 Carnac(seed): 0.106 Positive Predictive Value Mastr(20): 0.870 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.710 MCFold: 0.500 Sensitivity Mastr(20): 0.637 MCFold: 0.559 Positive Predictive Value Mastr(20): 0.796 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.225 RSpredict(seed): 0.179 Sensitivity Mastr(20): 0.061 RSpredict(seed): 0.090 Positive Predictive Value Mastr(20): 0.827 RSpredict(seed): 0.358 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.322 NanoFolder: 0.189 Sensitivity Mastr(20): 0.125 NanoFolder: 0.218 Positive Predictive Value Mastr(20): 0.832 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.265 Mastr(seed): 0.104 Sensitivity Mastr(20): 0.085 Mastr(seed): 0.013 Positive Predictive Value Mastr(20): 0.834 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(seed)	39 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.781 Murlet(seed): 0.630 Sensitivity TurboFold(seed): 0.750 Murlet(seed): 0.446 Positive Predictive Value TurboFold(seed): 0.814 Murlet(seed): 0.894 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.800 Murlet(seed): 0.540 Sensitivity PETfold_pre2.0(seed): 0.740 Murlet(seed): 0.360 Positive Predictive Value PETfold_pre2.0(seed): 0.866 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.761 Murlet(seed): 0.540 Sensitivity ContextFold: 0.727 Murlet(seed): 0.360 Positive Predictive Value ContextFold: 0.798 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.802 Murlet(seed): 0.631 Sensitivity TurboFold(20): 0.747 Murlet(seed): 0.418 Positive Predictive Value TurboFold(20): 0.864 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.817 Murlet(seed): 0.540 Sensitivity CentroidAlifold(seed): 0.728 Murlet(seed): 0.360 Positive Predictive Value CentroidAlifold(seed): 0.916 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 Murlet(seed): 0.631 Sensitivity PETfold_pre2.0(20): 0.618 Murlet(seed): 0.418 Positive Predictive Value PETfold_pre2.0(20): 0.882 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.804 Murlet(seed): 0.631 Sensitivity CentroidAlifold(20): 0.703 Murlet(seed): 0.418 Positive Predictive Value CentroidAlifold(20): 0.923 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.727 Murlet(seed): 0.519 Sensitivity CentroidHomfold‑LAST: 0.631 Murlet(seed): 0.322 Positive Predictive Value CentroidHomfold‑LAST: 0.840 Murlet(seed): 0.839 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.695 Murlet(seed): 0.631 Sensitivity PPfold(20): 0.546 Murlet(seed): 0.418 Positive Predictive Value PPfold(20): 0.889 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.672 Murlet(seed): 0.631 Sensitivity RNAalifold(20): 0.518 Murlet(seed): 0.418 Positive Predictive Value RNAalifold(20): 0.876 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.731 Murlet(seed): 0.540 Sensitivity MXScarna(seed): 0.700 Murlet(seed): 0.360 Positive Predictive Value MXScarna(seed): 0.763 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.839 Murlet(seed): 0.631 Sensitivity MXScarna(20): 0.803 Murlet(seed): 0.418 Positive Predictive Value MXScarna(20): 0.879 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.680 Murlet(seed): 0.540 Sensitivity IPknot: 0.639 Murlet(seed): 0.360 Positive Predictive Value IPknot: 0.725 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 Multilign(20) vs Murlet(seed) Matthews Correlation Coefficient Multilign(20): 0.673 Murlet(seed): 0.636 Sensitivity Multilign(20): 0.523 Murlet(seed): 0.428 Positive Predictive Value Multilign(20): 0.872 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.678 Murlet(seed): 0.631 Sensitivity Murlet(20): 0.513 Murlet(seed): 0.418 Positive Predictive Value Murlet(20): 0.899 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.725 Murlet(seed): 0.540 Sensitivity RNAalifold(seed): 0.592 Murlet(seed): 0.360 Positive Predictive Value RNAalifold(seed): 0.890 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.645 Murlet(seed): 0.540 Sensitivity CentroidFold: 0.594 Murlet(seed): 0.360 Positive Predictive Value CentroidFold: 0.701 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.643 Murlet(seed): 0.631 Sensitivity RNASampler(20): 0.454 Murlet(seed): 0.418 Positive Predictive Value RNASampler(20): 0.913 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 0.000579628272742	123 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.637 Murlet(seed): 0.540 Sensitivity Contrafold: 0.619 Murlet(seed): 0.360 Positive Predictive Value Contrafold: 0.657 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.613 Murlet(seed): 0.540 Sensitivity Sfold: 0.572 Murlet(seed): 0.360 Positive Predictive Value Sfold: 0.658 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.699 Murlet(seed): 0.656 Sensitivity Multilign(seed): 0.656 Murlet(seed): 0.480 Positive Predictive Value Multilign(seed): 0.746 Murlet(seed): 0.897 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	123 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.598 Murlet(seed): 0.540 Sensitivity MaxExpect: 0.585 Murlet(seed): 0.360 Positive Predictive Value MaxExpect: 0.613 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.595 Murlet(seed): 0.540 Sensitivity ProbKnot: 0.588 Murlet(seed): 0.360 Positive Predictive Value ProbKnot: 0.604 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.586 Murlet(seed): 0.540 Sensitivity Fold: 0.583 Murlet(seed): 0.360 Positive Predictive Value Fold: 0.591 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.629 Murlet(seed): 0.572 Sensitivity RNASampler(seed): 0.468 Murlet(seed): 0.369 Positive Predictive Value RNASampler(seed): 0.847 Murlet(seed): 0.889 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.600 Murlet(seed): 0.540 Sensitivity UNAFold: 0.593 Murlet(seed): 0.360 Positive Predictive Value UNAFold: 0.609 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.595 Murlet(seed): 0.519 Sensitivity RNAsubopt: 0.594 Murlet(seed): 0.322 Positive Predictive Value RNAsubopt: 0.597 Murlet(seed): 0.839 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RSpredict(20) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(20): 0.748 Murlet(seed): 0.631 Sensitivity RSpredict(20): 0.667 Murlet(seed): 0.418 Positive Predictive Value RSpredict(20): 0.844 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 5.23657817852e-08	45 CMfinder(20) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(20): 0.721 Murlet(seed): 0.631 Sensitivity CMfinder(20): 0.591 Murlet(seed): 0.418 Positive Predictive Value CMfinder(20): 0.884 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.598 Murlet(seed): 0.540 Sensitivity PknotsRG: 0.597 Murlet(seed): 0.360 Positive Predictive Value PknotsRG: 0.601 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 Murlet(seed) vs Carnac(20) Matthews Correlation Coefficient Murlet(seed): 0.631 Carnac(20): 0.444 Sensitivity Murlet(seed): 0.418 Carnac(20): 0.223 Positive Predictive Value Murlet(seed): 0.956 Carnac(20): 0.890 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 5.23657817852e-08	123 RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.596 Murlet(seed): 0.540 Sensitivity RNAfold: 0.590 Murlet(seed): 0.360 Positive Predictive Value RNAfold: 0.603 Murlet(seed): 0.811 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	99 Murlet(seed) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(seed): 0.555 CMfinder(seed): 0.531 Sensitivity Murlet(seed): 0.351 CMfinder(seed): 0.382 Positive Predictive Value Murlet(seed): 0.879 CMfinder(seed): 0.741 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 3.56938820447e-08	108 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.595 Murlet(seed): 0.553 Sensitivity Afold: 0.589 Murlet(seed): 0.371 Positive Predictive Value Afold: 0.601 Murlet(seed): 0.823 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.572 Murlet(seed): 0.477 Sensitivity HotKnots: 0.562 Murlet(seed): 0.277 Positive Predictive Value HotKnots: 0.588 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.540 CRWrnafold: 0.513 Sensitivity Murlet(seed): 0.360 CRWrnafold: 0.507 Positive Predictive Value Murlet(seed): 0.811 CRWrnafold: 0.520 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 6.06606238843e-08	71 Murlet(seed) vs Pknots Matthews Correlation Coefficient Murlet(seed): 0.451 Pknots: 0.444 Sensitivity Murlet(seed): 0.267 Pknots: 0.428 Positive Predictive Value Murlet(seed): 0.771 Pknots: 0.471 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 0.000150377120024	122 Murlet(seed) vs McQFold Matthews Correlation Coefficient Murlet(seed): 0.530 McQFold: 0.500 Sensitivity Murlet(seed): 0.336 McQFold: 0.480 Positive Predictive Value Murlet(seed): 0.839 McQFold: 0.523 Number of pairs reference - predicted secondary structure: 122 Wilcoxon single-rank test P-value: 3.85233844192e-08	119 RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.564 Murlet(seed): 0.511 Sensitivity RNAshapes: 0.559 Murlet(seed): 0.315 Positive Predictive Value RNAshapes: 0.571 Murlet(seed): 0.833 Number of pairs reference - predicted secondary structure: 119 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 PPfold(seed) vs Murlet(seed) Matthews Correlation Coefficient PPfold(seed): 0.742 Murlet(seed): 0.588 Sensitivity PPfold(seed): 0.657 Murlet(seed): 0.411 Positive Predictive Value PPfold(seed): 0.839 Murlet(seed): 0.842 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 Mastr(20) vs Murlet(seed) Matthews Correlation Coefficient Mastr(20): 0.697 Murlet(seed): 0.631 Sensitivity Mastr(20): 0.584 Murlet(seed): 0.418 Positive Predictive Value Mastr(20): 0.837 Murlet(seed): 0.956 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.519 RNASLOpt: 0.506 Sensitivity Murlet(seed): 0.322 RNASLOpt: 0.472 Positive Predictive Value Murlet(seed): 0.839 RNASLOpt: 0.545 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 2.71856013146e-06	= Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.516 Murlet(seed): 0.505 Sensitivity Cylofold: 0.469 Murlet(seed): 0.315 Positive Predictive Value Cylofold: 0.577 Murlet(seed): 0.817 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 0.0155447020429	+ Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.530 RNAwolf: 0.410 Sensitivity Murlet(seed): 0.336 RNAwolf: 0.418 Positive Predictive Value Murlet(seed): 0.839 RNAwolf: 0.404 Number of pairs reference - predicted secondary structure: 122 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs Vsfold4 Matthews Correlation Coefficient Murlet(seed): 0.519 Vsfold4: 0.290 Sensitivity Murlet(seed): 0.322 Vsfold4: 0.266 Positive Predictive Value Murlet(seed): 0.839 Vsfold4: 0.320 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.519 Vsfold5: 0.278 Sensitivity Murlet(seed): 0.322 Vsfold5: 0.263 Positive Predictive Value Murlet(seed): 0.839 Vsfold5: 0.297 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.456 Murlet(seed): 0.451 Sensitivity Alterna: 0.430 Murlet(seed): 0.267 Positive Predictive Value Alterna: 0.494 Murlet(seed): 0.771 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 0.115804103359	+ Murlet(seed) vs RDfolder Matthews Correlation Coefficient Murlet(seed): 0.451 RDfolder: 0.361 Sensitivity Murlet(seed): 0.267 RDfolder: 0.294 Positive Predictive Value Murlet(seed): 0.771 RDfolder: 0.455 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.530 Carnac(seed): 0.384 Sensitivity Murlet(seed): 0.336 Carnac(seed): 0.174 Positive Predictive Value Murlet(seed): 0.839 Carnac(seed): 0.850 Number of pairs reference - predicted secondary structure: 122 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.431 MCFold: 0.427 Sensitivity Murlet(seed): 0.236 MCFold: 0.470 Positive Predictive Value Murlet(seed): 0.793 MCFold: 0.396 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 0.397105643544	+ Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.540 RSpredict(seed): 0.519 Sensitivity Murlet(seed): 0.360 RSpredict(seed): 0.395 Positive Predictive Value Murlet(seed): 0.811 RSpredict(seed): 0.682 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.470 NanoFolder: 0.261 Sensitivity Murlet(seed): 0.254 NanoFolder: 0.304 Positive Predictive Value Murlet(seed): 0.871 NanoFolder: 0.229 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.530 Mastr(seed): 0.370 Sensitivity Murlet(seed): 0.336 Mastr(seed): 0.168 Positive Predictive Value Murlet(seed): 0.839 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 122 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASLOpt	50 TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.785 RNASLOpt: 0.522 Sensitivity TurboFold(seed): 0.758 RNASLOpt: 0.497 Positive Predictive Value TurboFold(seed): 0.814 RNASLOpt: 0.552 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	1059 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.747 RNASLOpt: 0.478 Sensitivity PETfold_pre2.0(seed): 0.670 RNASLOpt: 0.452 Positive Predictive Value PETfold_pre2.0(seed): 0.835 RNASLOpt: 0.509 Number of pairs reference - predicted secondary structure: 1059 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.755 RNASLOpt: 0.470 Sensitivity ContextFold: 0.717 RNASLOpt: 0.442 Positive Predictive Value ContextFold: 0.795 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.787 RNASLOpt: 0.500 Sensitivity TurboFold(20): 0.742 RNASLOpt: 0.464 Positive Predictive Value TurboFold(20): 0.837 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	581 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.736 RNASLOpt: 0.479 Sensitivity CentroidAlifold(seed): 0.596 RNASLOpt: 0.446 Positive Predictive Value CentroidAlifold(seed): 0.910 RNASLOpt: 0.517 Number of pairs reference - predicted secondary structure: 581 Wilcoxon single-rank test P-value: 3.56938820447e-08	544 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.769 RNASLOpt: 0.500 Sensitivity PETfold_pre2.0(20): 0.679 RNASLOpt: 0.463 Positive Predictive Value PETfold_pre2.0(20): 0.872 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 544 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.760 RNASLOpt: 0.500 Sensitivity CentroidAlifold(20): 0.624 RNASLOpt: 0.464 Positive Predictive Value CentroidAlifold(20): 0.928 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	1542 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.679 RNASLOpt: 0.471 Sensitivity CentroidHomfold‑LAST: 0.544 RNASLOpt: 0.444 Positive Predictive Value CentroidHomfold‑LAST: 0.847 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1542 Wilcoxon single-rank test P-value: 3.56938820447e-08	536 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.763 RNASLOpt: 0.501 Sensitivity PPfold(20): 0.656 RNASLOpt: 0.464 Positive Predictive Value PPfold(20): 0.888 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 536 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.710 RNASLOpt: 0.500 Sensitivity RNAalifold(20): 0.582 RNASLOpt: 0.464 Positive Predictive Value RNAalifold(20): 0.866 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	603 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.675 RNASLOpt: 0.480 Sensitivity MXScarna(seed): 0.587 RNASLOpt: 0.447 Positive Predictive Value MXScarna(seed): 0.778 RNASLOpt: 0.517 Number of pairs reference - predicted secondary structure: 603 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.703 RNASLOpt: 0.500 Sensitivity MXScarna(20): 0.637 RNASLOpt: 0.464 Positive Predictive Value MXScarna(20): 0.776 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.639 RNASLOpt: 0.470 Sensitivity IPknot: 0.591 RNASLOpt: 0.442 Positive Predictive Value IPknot: 0.691 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	520 Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.690 RNASLOpt: 0.506 Sensitivity Multilign(20): 0.623 RNASLOpt: 0.469 Positive Predictive Value Multilign(20): 0.765 RNASLOpt: 0.548 Number of pairs reference - predicted secondary structure: 520 Wilcoxon single-rank test P-value: 3.56938820447e-08	481 Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.640 RNASLOpt: 0.497 Sensitivity Murlet(20): 0.508 RNASLOpt: 0.462 Positive Predictive Value Murlet(20): 0.809 RNASLOpt: 0.538 Number of pairs reference - predicted secondary structure: 481 Wilcoxon single-rank test P-value: 3.56938820447e-08	571 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.558 RNASLOpt: 0.477 Sensitivity RNAalifold(seed): 0.361 RNASLOpt: 0.444 Positive Predictive Value RNAalifold(seed): 0.863 RNASLOpt: 0.515 Number of pairs reference - predicted secondary structure: 571 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.601 RNASLOpt: 0.470 Sensitivity CentroidFold: 0.555 RNASLOpt: 0.442 Positive Predictive Value CentroidFold: 0.653 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.676 RNASLOpt: 0.520 Sensitivity RNASampler(20): 0.522 RNASLOpt: 0.488 Positive Predictive Value RNASampler(20): 0.877 RNASLOpt: 0.557 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.589 RNASLOpt: 0.470 Sensitivity Contrafold: 0.579 RNASLOpt: 0.442 Positive Predictive Value Contrafold: 0.601 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.564 RNASLOpt: 0.470 Sensitivity Sfold: 0.518 RNASLOpt: 0.442 Positive Predictive Value Sfold: 0.615 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.681 RNASLOpt: 0.478 Sensitivity Multilign(seed): 0.649 RNASLOpt: 0.457 Positive Predictive Value Multilign(seed): 0.717 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	1543 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.566 RNASLOpt: 0.470 Sensitivity MaxExpect: 0.554 RNASLOpt: 0.442 Positive Predictive Value MaxExpect: 0.580 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.564 RNASLOpt: 0.470 Sensitivity ProbKnot: 0.560 RNASLOpt: 0.442 Positive Predictive Value ProbKnot: 0.571 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.547 RNASLOpt: 0.470 Sensitivity Fold: 0.548 RNASLOpt: 0.442 Positive Predictive Value Fold: 0.548 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): 0.629 RNASLOpt: 0.531 Sensitivity RNASampler(seed): 0.468 RNASLOpt: 0.485 Positive Predictive Value RNASampler(seed): 0.847 RNASLOpt: 0.585 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.535 RNASLOpt: 0.470 Sensitivity UNAFold: 0.530 RNASLOpt: 0.442 Positive Predictive Value UNAFold: 0.543 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	1542 RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.529 RNASLOpt: 0.471 Sensitivity RNAsubopt: 0.534 RNASLOpt: 0.444 Positive Predictive Value RNAsubopt: 0.526 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1542 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 RSpredict(20) vs RNASLOpt Matthews Correlation Coefficient RSpredict(20): 0.539 RNASLOpt: 0.500 Sensitivity RSpredict(20): 0.401 RNASLOpt: 0.464 Positive Predictive Value RSpredict(20): 0.725 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	543 CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.560 RNASLOpt: 0.499 Sensitivity CMfinder(20): 0.392 RNASLOpt: 0.463 Positive Predictive Value CMfinder(20): 0.801 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 543 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.531 RNASLOpt: 0.470 Sensitivity PknotsRG: 0.531 RNASLOpt: 0.442 Positive Predictive Value PknotsRG: 0.533 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.500 Carnac(20): 0.473 Sensitivity RNASLOpt: 0.464 Carnac(20): 0.252 Positive Predictive Value RNASLOpt: 0.542 Carnac(20): 0.889 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.534 RNASLOpt: 0.470 Sensitivity RNAfold: 0.534 RNASLOpt: 0.442 Positive Predictive Value RNAfold: 0.537 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	125 CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): 0.495 RNASLOpt: 0.489 Sensitivity CMfinder(seed): 0.325 RNASLOpt: 0.458 Positive Predictive Value CMfinder(seed): 0.755 RNASLOpt: 0.524 Number of pairs reference - predicted secondary structure: 125 Wilcoxon single-rank test P-value: 0.00297289556633	944 Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.541 RNASLOpt: 0.467 Sensitivity Afold: 0.534 RNASLOpt: 0.434 Positive Predictive Value Afold: 0.550 RNASLOpt: 0.505 Number of pairs reference - predicted secondary structure: 944 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.613 RNASLOpt: 0.562 Sensitivity HotKnots: 0.607 RNASLOpt: 0.520 Positive Predictive Value HotKnots: 0.624 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	1542 CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.487 RNASLOpt: 0.470 Sensitivity CRWrnafold: 0.486 RNASLOpt: 0.442 Positive Predictive Value CRWrnafold: 0.489 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1542 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.610 Pknots: 0.606 Sensitivity RNASLOpt: 0.566 Pknots: 0.595 Positive Predictive Value RNASLOpt: 0.665 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 8.67590017402e-07	1543 McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.480 RNASLOpt: 0.470 Sensitivity McQFold: 0.467 RNASLOpt: 0.442 Positive Predictive Value McQFold: 0.497 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	1533 RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.480 RNASLOpt: 0.471 Sensitivity RNAshapes: 0.475 RNASLOpt: 0.444 Positive Predictive Value RNAshapes: 0.486 RNASLOpt: 0.502 Number of pairs reference - predicted secondary structure: 1533 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 PPfold(seed) vs RNASLOpt Matthews Correlation Coefficient PPfold(seed): 0.635 RNASLOpt: 0.542 Sensitivity PPfold(seed): 0.511 RNASLOpt: 0.516 Positive Predictive Value PPfold(seed): 0.790 RNASLOpt: 0.572 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.500 Mastr(20): 0.364 Sensitivity RNASLOpt: 0.464 Mastr(20): 0.168 Positive Predictive Value RNASLOpt: 0.542 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.519 RNASLOpt: 0.506 Sensitivity Murlet(seed): 0.322 RNASLOpt: 0.472 Positive Predictive Value Murlet(seed): 0.839 RNASLOpt: 0.545 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 2.71856013146e-06		+ RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.594 Cylofold: 0.575 Sensitivity RNASLOpt: 0.548 Cylofold: 0.551 Positive Predictive Value RNASLOpt: 0.651 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.470 RNAwolf: 0.390 Sensitivity RNASLOpt: 0.442 RNAwolf: 0.403 Positive Predictive Value RNASLOpt: 0.502 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.471 Vsfold4: 0.349 Sensitivity RNASLOpt: 0.444 Vsfold4: 0.321 Positive Predictive Value RNASLOpt: 0.502 Vsfold4: 0.382 Number of pairs reference - predicted secondary structure: 1542 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.471 Vsfold5: 0.342 Sensitivity RNASLOpt: 0.444 Vsfold5: 0.325 Positive Predictive Value RNASLOpt: 0.502 Vsfold5: 0.361 Number of pairs reference - predicted secondary structure: 1542 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Alterna Matthews Correlation Coefficient RNASLOpt: 0.612 Alterna: 0.552 Sensitivity RNASLOpt: 0.567 Alterna: 0.547 Positive Predictive Value RNASLOpt: 0.667 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.612 RDfolder: 0.520 Sensitivity RNASLOpt: 0.567 RDfolder: 0.464 Positive Predictive Value RNASLOpt: 0.667 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.452 Carnac(seed): 0.240 Sensitivity RNASLOpt: 0.424 Carnac(seed): 0.065 Positive Predictive Value RNASLOpt: 0.484 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 239 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.577 MCFold: 0.473 Sensitivity RNASLOpt: 0.531 MCFold: 0.524 Positive Predictive Value RNASLOpt: 0.633 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.479 RSpredict(seed): 0.253 Sensitivity RNASLOpt: 0.446 RSpredict(seed): 0.118 Positive Predictive Value RNASLOpt: 0.517 RSpredict(seed): 0.544 Number of pairs reference - predicted secondary structure: 584 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.479 NanoFolder: 0.205 Sensitivity RNASLOpt: 0.446 NanoFolder: 0.239 Positive Predictive Value RNASLOpt: 0.517 NanoFolder: 0.178 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.479 Mastr(seed): 0.124 Sensitivity RNASLOpt: 0.446 Mastr(seed): 0.019 Positive Predictive Value RNASLOpt: 0.516 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 587 Wilcoxon single-rank test P-value: 3.56938820447e-08
Cylofold	32 TurboFold(seed) vs Cylofold Matthews Correlation Coefficient TurboFold(seed): 0.800 Cylofold: 0.653 Sensitivity TurboFold(seed): 0.770 Cylofold: 0.626 Positive Predictive Value TurboFold(seed): 0.833 Cylofold: 0.686 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	464 PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.881 Cylofold: 0.580 Sensitivity PETfold_pre2.0(seed): 0.828 Cylofold: 0.568 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Cylofold: 0.598 Number of pairs reference - predicted secondary structure: 464 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.805 Cylofold: 0.575 Sensitivity ContextFold: 0.765 Cylofold: 0.551 Positive Predictive Value ContextFold: 0.851 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.892 Cylofold: 0.557 Sensitivity TurboFold(20): 0.864 Cylofold: 0.543 Positive Predictive Value TurboFold(20): 0.922 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.785 Cylofold: 0.518 Sensitivity CentroidAlifold(seed): 0.694 Cylofold: 0.491 Positive Predictive Value CentroidAlifold(seed): 0.892 Cylofold: 0.552 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.845 Cylofold: 0.557 Sensitivity PETfold_pre2.0(20): 0.735 Cylofold: 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.974 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Cylofold: 0.557 Sensitivity CentroidAlifold(20): 0.753 Cylofold: 0.543 Positive Predictive Value CentroidAlifold(20): 0.959 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.765 Cylofold: 0.575 Sensitivity CentroidHomfold‑LAST: 0.706 Cylofold: 0.551 Positive Predictive Value CentroidHomfold‑LAST: 0.832 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	298 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.837 Cylofold: 0.560 Sensitivity PPfold(20): 0.719 Cylofold: 0.546 Positive Predictive Value PPfold(20): 0.976 Cylofold: 0.579 Number of pairs reference - predicted secondary structure: 298 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.816 Cylofold: 0.557 Sensitivity RNAalifold(20): 0.690 Cylofold: 0.543 Positive Predictive Value RNAalifold(20): 0.968 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	214 MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.760 Cylofold: 0.520 Sensitivity MXScarna(seed): 0.725 Cylofold: 0.495 Positive Predictive Value MXScarna(seed): 0.801 Cylofold: 0.552 Number of pairs reference - predicted secondary structure: 214 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.841 Cylofold: 0.557 Sensitivity MXScarna(20): 0.795 Cylofold: 0.543 Positive Predictive Value MXScarna(20): 0.892 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.718 Cylofold: 0.575 Sensitivity IPknot: 0.686 Cylofold: 0.551 Positive Predictive Value IPknot: 0.757 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	295 Multilign(20) vs Cylofold Matthews Correlation Coefficient Multilign(20): 0.783 Cylofold: 0.563 Sensitivity Multilign(20): 0.695 Cylofold: 0.549 Positive Predictive Value Multilign(20): 0.884 Cylofold: 0.583 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	303 Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.751 Cylofold: 0.558 Sensitivity Murlet(20): 0.620 Cylofold: 0.544 Positive Predictive Value Murlet(20): 0.913 Cylofold: 0.578 Number of pairs reference - predicted secondary structure: 303 Wilcoxon single-rank test P-value: 3.56938820447e-08	187 RNAalifold(seed) vs Cylofold Matthews Correlation Coefficient RNAalifold(seed): 0.578 Cylofold: 0.512 Sensitivity RNAalifold(seed): 0.370 Cylofold: 0.484 Positive Predictive Value RNAalifold(seed): 0.909 Cylofold: 0.548 Number of pairs reference - predicted secondary structure: 187 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.675 Cylofold: 0.575 Sensitivity CentroidFold: 0.640 Cylofold: 0.551 Positive Predictive Value CentroidFold: 0.717 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	299 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.773 Cylofold: 0.559 Sensitivity RNASampler(20): 0.625 Cylofold: 0.546 Positive Predictive Value RNASampler(20): 0.959 Cylofold: 0.579 Number of pairs reference - predicted secondary structure: 299 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.673 Cylofold: 0.575 Sensitivity Contrafold: 0.662 Cylofold: 0.551 Positive Predictive Value Contrafold: 0.689 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.642 Cylofold: 0.575 Sensitivity Sfold: 0.603 Cylofold: 0.551 Positive Predictive Value Sfold: 0.688 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.766 Multilign(seed): 0.475 Sensitivity Cylofold: 0.719 Multilign(seed): 0.372 Positive Predictive Value Cylofold: 0.822 Multilign(seed): 0.617 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.34193807955e-08	798 MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.660 Cylofold: 0.575 Sensitivity MaxExpect: 0.642 Cylofold: 0.551 Positive Predictive Value MaxExpect: 0.683 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.658 Cylofold: 0.575 Sensitivity ProbKnot: 0.649 Cylofold: 0.551 Positive Predictive Value ProbKnot: 0.673 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.654 Cylofold: 0.575 Sensitivity Fold: 0.644 Cylofold: 0.551 Positive Predictive Value Fold: 0.669 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 RNASampler(seed) vs Cylofold Matthews Correlation Coefficient RNASampler(seed): 0.514 Cylofold: 0.503 Sensitivity RNASampler(seed): 0.335 Cylofold: 0.455 Positive Predictive Value RNASampler(seed): 0.797 Cylofold: 0.565 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 1.80472700427e-05	798 UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.639 Cylofold: 0.575 Sensitivity UNAFold: 0.624 Cylofold: 0.551 Positive Predictive Value UNAFold: 0.661 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.639 Cylofold: 0.575 Sensitivity RNAsubopt: 0.631 Cylofold: 0.551 Positive Predictive Value RNAsubopt: 0.652 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 RSpredict(20) vs Cylofold Matthews Correlation Coefficient RSpredict(20): 0.794 Cylofold: 0.557 Sensitivity RSpredict(20): 0.700 Cylofold: 0.543 Positive Predictive Value RSpredict(20): 0.903 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	300 CMfinder(20) vs Cylofold Matthews Correlation Coefficient CMfinder(20): 0.741 Cylofold: 0.559 Sensitivity CMfinder(20): 0.610 Cylofold: 0.546 Positive Predictive Value CMfinder(20): 0.903 Cylofold: 0.578 Number of pairs reference - predicted secondary structure: 300 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.637 Cylofold: 0.575 Sensitivity PknotsRG: 0.628 Cylofold: 0.551 Positive Predictive Value PknotsRG: 0.652 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 Carnac(20) vs Cylofold Matthews Correlation Coefficient Carnac(20): 0.676 Cylofold: 0.557 Sensitivity Carnac(20): 0.499 Cylofold: 0.543 Positive Predictive Value Carnac(20): 0.918 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.635 Cylofold: 0.575 Sensitivity RNAfold: 0.624 Cylofold: 0.551 Positive Predictive Value RNAfold: 0.651 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	67 CMfinder(seed) vs Cylofold Matthews Correlation Coefficient CMfinder(seed): 0.599 Cylofold: 0.465 Sensitivity CMfinder(seed): 0.469 Cylofold: 0.415 Positive Predictive Value CMfinder(seed): 0.772 Cylofold: 0.531 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	481 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.580 Cylofold: 0.540 Sensitivity Afold: 0.561 Cylofold: 0.503 Positive Predictive Value Afold: 0.607 Cylofold: 0.588 Number of pairs reference - predicted secondary structure: 481 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.638 Cylofold: 0.577 Sensitivity HotKnots: 0.631 Cylofold: 0.554 Positive Predictive Value HotKnots: 0.651 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	797 CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.665 Cylofold: 0.574 Sensitivity CRWrnafold: 0.649 Cylofold: 0.551 Positive Predictive Value CRWrnafold: 0.686 Cylofold: 0.605 Number of pairs reference - predicted secondary structure: 797 Wilcoxon single-rank test P-value: 3.56938820447e-08	676 Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.621 Pknots: 0.614 Sensitivity Cylofold: 0.599 Pknots: 0.603 Positive Predictive Value Cylofold: 0.650 Pknots: 0.632 Number of pairs reference - predicted secondary structure: 676 Wilcoxon single-rank test P-value: 6.06606238843e-08	798 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.616 Cylofold: 0.575 Sensitivity McQFold: 0.587 Cylofold: 0.551 Positive Predictive Value McQFold: 0.653 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.632 Cylofold: 0.575 Sensitivity RNAshapes: 0.621 Cylofold: 0.551 Positive Predictive Value RNAshapes: 0.649 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.624 PPfold(seed): 0.375 Sensitivity Cylofold: 0.593 PPfold(seed): 0.167 Positive Predictive Value Cylofold: 0.661 PPfold(seed): 0.845 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 Mastr(20) vs Cylofold Matthews Correlation Coefficient Mastr(20): 0.713 Cylofold: 0.557 Sensitivity Mastr(20): 0.641 Cylofold: 0.543 Positive Predictive Value Mastr(20): 0.796 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	80 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.516 Murlet(seed): 0.505 Sensitivity Cylofold: 0.469 Murlet(seed): 0.315 Positive Predictive Value Cylofold: 0.577 Murlet(seed): 0.817 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 0.0155447020429	798 RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.594 Cylofold: 0.575 Sensitivity RNASLOpt: 0.548 Cylofold: 0.551 Positive Predictive Value RNASLOpt: 0.651 Cylofold: 0.606 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.575 RNAwolf: 0.543 Sensitivity Cylofold: 0.551 RNAwolf: 0.546 Positive Predictive Value Cylofold: 0.606 RNAwolf: 0.547 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.575 Vsfold4: 0.513 Sensitivity Cylofold: 0.551 Vsfold4: 0.470 Positive Predictive Value Cylofold: 0.606 Vsfold4: 0.567 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.575 Vsfold5: 0.497 Sensitivity Cylofold: 0.551 Vsfold5: 0.468 Positive Predictive Value Cylofold: 0.606 Vsfold5: 0.535 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.621 Alterna: 0.555 Sensitivity Cylofold: 0.599 Alterna: 0.549 Positive Predictive Value Cylofold: 0.650 Alterna: 0.569 Number of pairs reference - predicted secondary structure: 673 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.621 RDfolder: 0.528 Sensitivity Cylofold: 0.599 RDfolder: 0.470 Positive Predictive Value Cylofold: 0.650 RDfolder: 0.601 Number of pairs reference - predicted secondary structure: 673 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.541 Carnac(seed): 0.408 Sensitivity Cylofold: 0.502 Carnac(seed): 0.189 Positive Predictive Value Cylofold: 0.591 Carnac(seed): 0.888 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.584 MCFold: 0.487 Sensitivity Cylofold: 0.559 MCFold: 0.542 Positive Predictive Value Cylofold: 0.617 MCFold: 0.447 Number of pairs reference - predicted secondary structure: 714 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.518 RSpredict(seed): 0.402 Sensitivity Cylofold: 0.491 RSpredict(seed): 0.279 Positive Predictive Value Cylofold: 0.552 RSpredict(seed): 0.588 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.562 NanoFolder: 0.341 Sensitivity Cylofold: 0.530 NanoFolder: 0.392 Positive Predictive Value Cylofold: 0.602 NanoFolder: 0.306 Number of pairs reference - predicted secondary structure: 110 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.520 Mastr(seed): 0.285 Sensitivity Cylofold: 0.495 Mastr(seed): 0.101 Positive Predictive Value Cylofold: 0.553 Mastr(seed): 0.807 Number of pairs reference - predicted secondary structure: 215 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAwolf	51 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.791 RNAwolf: 0.422 Sensitivity TurboFold(seed): 0.762 RNAwolf: 0.433 Positive Predictive Value TurboFold(seed): 0.822 RNAwolf: 0.414 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	1141 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 RNAwolf: 0.379 Sensitivity PETfold_pre2.0(seed): 0.646 RNAwolf: 0.393 Positive Predictive Value PETfold_pre2.0(seed): 0.827 RNAwolf: 0.367 Number of pairs reference - predicted secondary structure: 1141 Wilcoxon single-rank test P-value: 3.56938820447e-08	1788 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.724 RNAwolf: 0.343 Sensitivity ContextFold: 0.687 RNAwolf: 0.358 Positive Predictive Value ContextFold: 0.763 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.787 RNAwolf: 0.414 Sensitivity TurboFold(20): 0.740 RNAwolf: 0.423 Positive Predictive Value TurboFold(20): 0.837 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.719 RNAwolf: 0.395 Sensitivity CentroidAlifold(seed): 0.571 RNAwolf: 0.404 Positive Predictive Value CentroidAlifold(seed): 0.905 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	562 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.766 RNAwolf: 0.414 Sensitivity PETfold_pre2.0(20): 0.675 RNAwolf: 0.423 Positive Predictive Value PETfold_pre2.0(20): 0.870 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 562 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.757 RNAwolf: 0.414 Sensitivity CentroidAlifold(20): 0.618 RNAwolf: 0.423 Positive Predictive Value CentroidAlifold(20): 0.928 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 RNAwolf: 0.384 Sensitivity CentroidHomfold‑LAST: 0.527 RNAwolf: 0.397 Positive Predictive Value CentroidHomfold‑LAST: 0.850 RNAwolf: 0.373 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	552 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.759 RNAwolf: 0.415 Sensitivity PPfold(20): 0.652 RNAwolf: 0.424 Positive Predictive Value PPfold(20): 0.885 RNAwolf: 0.409 Number of pairs reference - predicted secondary structure: 552 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.705 RNAwolf: 0.414 Sensitivity RNAalifold(20): 0.577 RNAwolf: 0.423 Positive Predictive Value RNAalifold(20): 0.863 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	664 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.651 RNAwolf: 0.395 Sensitivity MXScarna(seed): 0.556 RNAwolf: 0.405 Positive Predictive Value MXScarna(seed): 0.764 RNAwolf: 0.388 Number of pairs reference - predicted secondary structure: 664 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.701 RNAwolf: 0.414 Sensitivity MXScarna(20): 0.634 RNAwolf: 0.423 Positive Predictive Value MXScarna(20): 0.776 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	1788 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.599 RNAwolf: 0.343 Sensitivity IPknot: 0.542 RNAwolf: 0.358 Positive Predictive Value IPknot: 0.663 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	534 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.685 RNAwolf: 0.416 Sensitivity Multilign(20): 0.617 RNAwolf: 0.425 Positive Predictive Value Multilign(20): 0.762 RNAwolf: 0.410 Number of pairs reference - predicted secondary structure: 534 Wilcoxon single-rank test P-value: 3.56938820447e-08	495 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.631 RNAwolf: 0.417 Sensitivity Murlet(20): 0.496 RNAwolf: 0.428 Positive Predictive Value Murlet(20): 0.803 RNAwolf: 0.410 Number of pairs reference - predicted secondary structure: 495 Wilcoxon single-rank test P-value: 3.56938820447e-08	632 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.548 RNAwolf: 0.394 Sensitivity RNAalifold(seed): 0.350 RNAwolf: 0.404 Positive Predictive Value RNAalifold(seed): 0.859 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 632 Wilcoxon single-rank test P-value: 3.56938820447e-08	1788 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.570 RNAwolf: 0.343 Sensitivity CentroidFold: 0.515 RNAwolf: 0.358 Positive Predictive Value CentroidFold: 0.632 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.676 RNAwolf: 0.445 Sensitivity RNASampler(20): 0.522 RNAwolf: 0.457 Positive Predictive Value RNASampler(20): 0.877 RNAwolf: 0.437 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1788 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.558 RNAwolf: 0.343 Sensitivity Contrafold: 0.544 RNAwolf: 0.358 Positive Predictive Value Contrafold: 0.574 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	1788 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.525 RNAwolf: 0.343 Sensitivity Sfold: 0.477 RNAwolf: 0.358 Positive Predictive Value Sfold: 0.579 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.681 RNAwolf: 0.354 Sensitivity Multilign(seed): 0.649 RNAwolf: 0.368 Positive Predictive Value Multilign(seed): 0.717 RNAwolf: 0.342 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	1788 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.526 RNAwolf: 0.343 Sensitivity MaxExpect: 0.513 RNAwolf: 0.358 Positive Predictive Value MaxExpect: 0.540 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	1788 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.522 RNAwolf: 0.343 Sensitivity ProbKnot: 0.520 RNAwolf: 0.358 Positive Predictive Value ProbKnot: 0.526 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	1788 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.501 RNAwolf: 0.343 Sensitivity Fold: 0.504 RNAwolf: 0.358 Positive Predictive Value Fold: 0.498 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.629 RNAwolf: 0.354 Sensitivity RNASampler(seed): 0.468 RNAwolf: 0.360 Positive Predictive Value RNASampler(seed): 0.847 RNAwolf: 0.352 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	1788 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.492 RNAwolf: 0.343 Sensitivity UNAFold: 0.489 RNAwolf: 0.358 Positive Predictive Value UNAFold: 0.496 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	1641 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.525 RNAwolf: 0.384 Sensitivity RNAsubopt: 0.530 RNAwolf: 0.397 Positive Predictive Value RNAsubopt: 0.521 RNAwolf: 0.373 Number of pairs reference - predicted secondary structure: 1641 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.524 RNAwolf: 0.414 Sensitivity RSpredict(20): 0.385 RNAwolf: 0.423 Positive Predictive Value RSpredict(20): 0.714 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	561 CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.549 RNAwolf: 0.414 Sensitivity CMfinder(20): 0.380 RNAwolf: 0.423 Positive Predictive Value CMfinder(20): 0.794 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	1788 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.489 RNAwolf: 0.343 Sensitivity PknotsRG: 0.491 RNAwolf: 0.358 Positive Predictive Value PknotsRG: 0.488 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.469 RNAwolf: 0.414 Sensitivity Carnac(20): 0.248 RNAwolf: 0.423 Positive Predictive Value Carnac(20): 0.888 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	1788 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.487 RNAwolf: 0.343 Sensitivity RNAfold: 0.489 RNAwolf: 0.358 Positive Predictive Value RNAfold: 0.487 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1788 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.486 RNAwolf: 0.414 Sensitivity CMfinder(seed): 0.312 RNAwolf: 0.424 Positive Predictive Value CMfinder(seed): 0.757 RNAwolf: 0.406 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	1126 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.482 RNAwolf: 0.339 Sensitivity Afold: 0.479 RNAwolf: 0.352 Positive Predictive Value Afold: 0.486 RNAwolf: 0.328 Number of pairs reference - predicted secondary structure: 1126 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.613 RNAwolf: 0.518 Sensitivity HotKnots: 0.607 RNAwolf: 0.523 Positive Predictive Value HotKnots: 0.624 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	1787 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.440 RNAwolf: 0.343 Sensitivity CRWrnafold: 0.444 RNAwolf: 0.358 Positive Predictive Value CRWrnafold: 0.438 RNAwolf: 0.330 Number of pairs reference - predicted secondary structure: 1787 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.606 RNAwolf: 0.550 Sensitivity Pknots: 0.595 RNAwolf: 0.554 Positive Predictive Value Pknots: 0.624 RNAwolf: 0.554 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	1707 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.467 RNAwolf: 0.371 Sensitivity McQFold: 0.457 RNAwolf: 0.386 Positive Predictive Value McQFold: 0.480 RNAwolf: 0.358 Number of pairs reference - predicted secondary structure: 1707 Wilcoxon single-rank test P-value: 3.56938820447e-08	1588 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.477 RNAwolf: 0.388 Sensitivity RNAshapes: 0.472 RNAwolf: 0.402 Positive Predictive Value RNAshapes: 0.484 RNAwolf: 0.378 Number of pairs reference - predicted secondary structure: 1588 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 PPfold(seed) vs RNAwolf Matthews Correlation Coefficient PPfold(seed): 0.626 RNAwolf: 0.461 Sensitivity PPfold(seed): 0.495 RNAwolf: 0.477 Positive Predictive Value PPfold(seed): 0.794 RNAwolf: 0.448 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	565 RNAwolf vs Mastr(20) Matthews Correlation Coefficient RNAwolf: 0.414 Mastr(20): 0.350 Sensitivity RNAwolf: 0.423 Mastr(20): 0.156 Positive Predictive Value RNAwolf: 0.408 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 565 Wilcoxon single-rank test P-value: 3.56938820447e-08	122 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.530 RNAwolf: 0.410 Sensitivity Murlet(seed): 0.336 RNAwolf: 0.418 Positive Predictive Value Murlet(seed): 0.839 RNAwolf: 0.404 Number of pairs reference - predicted secondary structure: 122 Wilcoxon single-rank test P-value: 3.56938820447e-08	1543 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.470 RNAwolf: 0.390 Sensitivity RNASLOpt: 0.442 RNAwolf: 0.403 Positive Predictive Value RNASLOpt: 0.502 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 1543 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.575 RNAwolf: 0.543 Sensitivity Cylofold: 0.551 RNAwolf: 0.546 Positive Predictive Value Cylofold: 0.606 RNAwolf: 0.547 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAwolf vs Vsfold4 Matthews Correlation Coefficient RNAwolf: 0.386 Vsfold4: 0.346 Sensitivity RNAwolf: 0.400 Vsfold4: 0.318 Positive Predictive Value RNAwolf: 0.376 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.387 Vsfold5: 0.339 Sensitivity RNAwolf: 0.401 Vsfold5: 0.322 Positive Predictive Value RNAwolf: 0.377 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: 0.552 RNAwolf: 0.551 Sensitivity Alterna: 0.547 RNAwolf: 0.555 Positive Predictive Value Alterna: 0.566 RNAwolf: 0.555 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 0.0853441262641	+ RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.551 RDfolder: 0.520 Sensitivity RNAwolf: 0.555 RDfolder: 0.464 Positive Predictive Value RNAwolf: 0.555 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.369 Carnac(seed): 0.215 Sensitivity RNAwolf: 0.382 Carnac(seed): 0.055 Positive Predictive Value RNAwolf: 0.358 Carnac(seed): 0.850 Number of pairs reference - predicted secondary structure: 268 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: 0.530 MCFold: 0.473 Sensitivity RNAwolf: 0.532 MCFold: 0.524 Positive Predictive Value RNAwolf: 0.534 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.394 RSpredict(seed): 0.237 Sensitivity RNAwolf: 0.404 RSpredict(seed): 0.107 Positive Predictive Value RNAwolf: 0.387 RSpredict(seed): 0.528 Number of pairs reference - predicted secondary structure: 645 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.395 NanoFolder: 0.194 Sensitivity RNAwolf: 0.405 NanoFolder: 0.229 Positive Predictive Value RNAwolf: 0.386 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.394 Mastr(seed): 0.115 Sensitivity RNAwolf: 0.404 Mastr(seed): 0.016 Positive Predictive Value RNAwolf: 0.386 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold4	50 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.785 Vsfold4: 0.215 Sensitivity TurboFold(seed): 0.758 Vsfold4: 0.197 Positive Predictive Value TurboFold(seed): 0.814 Vsfold4: 0.239 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	1113 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 Vsfold4: 0.345 Sensitivity PETfold_pre2.0(seed): 0.655 Vsfold4: 0.318 Positive Predictive Value PETfold_pre2.0(seed): 0.827 Vsfold4: 0.377 Number of pairs reference - predicted secondary structure: 1113 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.751 Vsfold4: 0.346 Sensitivity ContextFold: 0.713 Vsfold4: 0.318 Positive Predictive Value ContextFold: 0.791 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	560 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.787 Vsfold4: 0.390 Sensitivity TurboFold(20): 0.740 Vsfold4: 0.356 Positive Predictive Value TurboFold(20): 0.837 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	614 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.726 Vsfold4: 0.338 Sensitivity CentroidAlifold(seed): 0.583 Vsfold4: 0.307 Positive Predictive Value CentroidAlifold(seed): 0.905 Vsfold4: 0.375 Number of pairs reference - predicted secondary structure: 614 Wilcoxon single-rank test P-value: 3.56938820447e-08	557 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.767 Vsfold4: 0.393 Sensitivity PETfold_pre2.0(20): 0.676 Vsfold4: 0.357 Positive Predictive Value PETfold_pre2.0(20): 0.871 Vsfold4: 0.434 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	560 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.758 Vsfold4: 0.390 Sensitivity CentroidAlifold(20): 0.620 Vsfold4: 0.356 Positive Predictive Value CentroidAlifold(20): 0.928 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.673 Vsfold4: 0.346 Sensitivity CentroidHomfold‑LAST: 0.534 Vsfold4: 0.318 Positive Predictive Value CentroidHomfold‑LAST: 0.850 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	548 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.761 Vsfold4: 0.392 Sensitivity PPfold(20): 0.654 Vsfold4: 0.357 Positive Predictive Value PPfold(20): 0.887 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 548 Wilcoxon single-rank test P-value: 3.56938820447e-08	560 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.707 Vsfold4: 0.390 Sensitivity RNAalifold(20): 0.579 Vsfold4: 0.356 Positive Predictive Value RNAalifold(20): 0.865 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	636 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.662 Vsfold4: 0.341 Sensitivity MXScarna(seed): 0.570 Vsfold4: 0.309 Positive Predictive Value MXScarna(seed): 0.770 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 636 Wilcoxon single-rank test P-value: 3.56938820447e-08	560 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.702 Vsfold4: 0.390 Sensitivity MXScarna(20): 0.635 Vsfold4: 0.356 Positive Predictive Value MXScarna(20): 0.777 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.636 Vsfold4: 0.346 Sensitivity IPknot: 0.588 Vsfold4: 0.318 Positive Predictive Value IPknot: 0.688 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.685 Vsfold4: 0.400 Sensitivity Multilign(20): 0.617 Vsfold4: 0.364 Positive Predictive Value Multilign(20): 0.761 Vsfold4: 0.441 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	491 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.634 Vsfold4: 0.391 Sensitivity Murlet(20): 0.500 Vsfold4: 0.357 Positive Predictive Value Murlet(20): 0.805 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 491 Wilcoxon single-rank test P-value: 3.56938820447e-08	604 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.551 Vsfold4: 0.336 Sensitivity RNAalifold(seed): 0.354 Vsfold4: 0.305 Positive Predictive Value RNAalifold(seed): 0.859 Vsfold4: 0.373 Number of pairs reference - predicted secondary structure: 604 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.599 Vsfold4: 0.346 Sensitivity CentroidFold: 0.553 Vsfold4: 0.318 Positive Predictive Value CentroidFold: 0.651 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.676 Vsfold4: 0.356 Sensitivity RNASampler(20): 0.522 Vsfold4: 0.330 Positive Predictive Value RNASampler(20): 0.877 Vsfold4: 0.388 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.586 Vsfold4: 0.346 Sensitivity Contrafold: 0.576 Vsfold4: 0.318 Positive Predictive Value Contrafold: 0.598 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.561 Vsfold4: 0.346 Sensitivity Sfold: 0.515 Vsfold4: 0.318 Positive Predictive Value Sfold: 0.613 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.681 Vsfold4: 0.205 Sensitivity Multilign(seed): 0.649 Vsfold4: 0.194 Positive Predictive Value Multilign(seed): 0.717 Vsfold4: 0.221 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	1612 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.562 Vsfold4: 0.346 Sensitivity MaxExpect: 0.550 Vsfold4: 0.318 Positive Predictive Value MaxExpect: 0.576 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.561 Vsfold4: 0.346 Sensitivity ProbKnot: 0.556 Vsfold4: 0.318 Positive Predictive Value ProbKnot: 0.567 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.544 Vsfold4: 0.346 Sensitivity Fold: 0.545 Vsfold4: 0.318 Positive Predictive Value Fold: 0.544 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.629 Vsfold4: 0.349 Sensitivity RNASampler(seed): 0.468 Vsfold4: 0.318 Positive Predictive Value RNASampler(seed): 0.847 Vsfold4: 0.388 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.532 Vsfold4: 0.346 Sensitivity UNAFold: 0.527 Vsfold4: 0.318 Positive Predictive Value UNAFold: 0.539 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.525 Vsfold4: 0.346 Sensitivity RNAsubopt: 0.530 Vsfold4: 0.318 Positive Predictive Value RNAsubopt: 0.521 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	560 RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.529 Vsfold4: 0.390 Sensitivity RSpredict(20): 0.391 Vsfold4: 0.356 Positive Predictive Value RSpredict(20): 0.718 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	556 CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.554 Vsfold4: 0.391 Sensitivity CMfinder(20): 0.385 Vsfold4: 0.357 Positive Predictive Value CMfinder(20): 0.798 Vsfold4: 0.432 Number of pairs reference - predicted secondary structure: 556 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.529 Vsfold4: 0.346 Sensitivity PknotsRG: 0.529 Vsfold4: 0.318 Positive Predictive Value PknotsRG: 0.531 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	560 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.470 Vsfold4: 0.390 Sensitivity Carnac(20): 0.249 Vsfold4: 0.356 Positive Predictive Value Carnac(20): 0.889 Vsfold4: 0.431 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.531 Vsfold4: 0.346 Sensitivity RNAfold: 0.531 Vsfold4: 0.318 Positive Predictive Value RNAfold: 0.533 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 CMfinder(seed) vs Vsfold4 Matthews Correlation Coefficient CMfinder(seed): 0.488 Vsfold4: 0.303 Sensitivity CMfinder(seed): 0.316 Vsfold4: 0.277 Positive Predictive Value CMfinder(seed): 0.755 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	978 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.538 Vsfold4: 0.344 Sensitivity Afold: 0.531 Vsfold4: 0.313 Positive Predictive Value Afold: 0.546 Vsfold4: 0.380 Number of pairs reference - predicted secondary structure: 978 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.613 Vsfold4: 0.486 Sensitivity HotKnots: 0.607 Vsfold4: 0.446 Positive Predictive Value HotKnots: 0.624 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	1611 CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.481 Vsfold4: 0.346 Sensitivity CRWrnafold: 0.482 Vsfold4: 0.318 Positive Predictive Value CRWrnafold: 0.483 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1611 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.606 Vsfold4: 0.592 Sensitivity Pknots: 0.595 Vsfold4: 0.544 Positive Predictive Value Pknots: 0.624 Vsfold4: 0.651 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.480 Vsfold4: 0.346 Sensitivity McQFold: 0.467 Vsfold4: 0.318 Positive Predictive Value McQFold: 0.495 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08	1584 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.476 Vsfold4: 0.349 Sensitivity RNAshapes: 0.472 Vsfold4: 0.321 Positive Predictive Value RNAshapes: 0.483 Vsfold4: 0.382 Number of pairs reference - predicted secondary structure: 1584 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): 0.635 Vsfold4: 0.244 Sensitivity PPfold(seed): 0.511 Vsfold4: 0.225 Positive Predictive Value PPfold(seed): 0.790 Vsfold4: 0.268 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	560 Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.390 Mastr(20): 0.354 Sensitivity Vsfold4: 0.356 Mastr(20): 0.159 Positive Predictive Value Vsfold4: 0.431 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 560 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 Murlet(seed) vs Vsfold4 Matthews Correlation Coefficient Murlet(seed): 0.519 Vsfold4: 0.290 Sensitivity Murlet(seed): 0.322 Vsfold4: 0.266 Positive Predictive Value Murlet(seed): 0.839 Vsfold4: 0.320 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	1542 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.471 Vsfold4: 0.349 Sensitivity RNASLOpt: 0.444 Vsfold4: 0.321 Positive Predictive Value RNASLOpt: 0.502 Vsfold4: 0.382 Number of pairs reference - predicted secondary structure: 1542 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.575 Vsfold4: 0.513 Sensitivity Cylofold: 0.551 Vsfold4: 0.470 Positive Predictive Value Cylofold: 0.606 Vsfold4: 0.567 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	1612 RNAwolf vs Vsfold4 Matthews Correlation Coefficient RNAwolf: 0.386 Vsfold4: 0.346 Sensitivity RNAwolf: 0.400 Vsfold4: 0.318 Positive Predictive Value RNAwolf: 0.376 Vsfold4: 0.378 Number of pairs reference - predicted secondary structure: 1612 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.347 Vsfold5: 0.339 Sensitivity Vsfold4: 0.319 Vsfold5: 0.322 Positive Predictive Value Vsfold4: 0.379 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.596 Alterna: 0.552 Sensitivity Vsfold4: 0.547 Alterna: 0.547 Positive Predictive Value Vsfold4: 0.656 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.596 RDfolder: 0.520 Sensitivity Vsfold4: 0.547 RDfolder: 0.464 Positive Predictive Value Vsfold4: 0.656 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.251 Carnac(seed): 0.231 Sensitivity Vsfold4: 0.231 Carnac(seed): 0.061 Positive Predictive Value Vsfold4: 0.277 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 247 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.500 MCFold: 0.473 Sensitivity Vsfold4: 0.456 MCFold: 0.524 Positive Predictive Value Vsfold4: 0.555 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.339 RSpredict(seed): 0.241 Sensitivity Vsfold4: 0.307 RSpredict(seed): 0.109 Positive Predictive Value Vsfold4: 0.376 RSpredict(seed): 0.533 Number of pairs reference - predicted secondary structure: 617 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.348 NanoFolder: 0.200 Sensitivity Vsfold4: 0.318 NanoFolder: 0.236 Positive Predictive Value Vsfold4: 0.384 NanoFolder: 0.173 Number of pairs reference - predicted secondary structure: 246 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.334 Mastr(seed): 0.119 Sensitivity Vsfold4: 0.303 Mastr(seed): 0.017 Positive Predictive Value Vsfold4: 0.369 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 615 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold5	50 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.785 Vsfold5: 0.260 Sensitivity TurboFold(seed): 0.758 Vsfold5: 0.250 Positive Predictive Value TurboFold(seed): 0.814 Vsfold5: 0.274 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	1106 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 Vsfold5: 0.333 Sensitivity PETfold_pre2.0(seed): 0.656 Vsfold5: 0.317 Positive Predictive Value PETfold_pre2.0(seed): 0.827 Vsfold5: 0.352 Number of pairs reference - predicted secondary structure: 1106 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.752 Vsfold5: 0.339 Sensitivity ContextFold: 0.715 Vsfold5: 0.322 Positive Predictive Value ContextFold: 0.793 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	557 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.787 Vsfold5: 0.365 Sensitivity TurboFold(20): 0.740 Vsfold5: 0.341 Positive Predictive Value TurboFold(20): 0.837 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	609 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.727 Vsfold5: 0.314 Sensitivity CentroidAlifold(seed): 0.584 Vsfold5: 0.293 Positive Predictive Value CentroidAlifold(seed): 0.905 Vsfold5: 0.339 Number of pairs reference - predicted secondary structure: 609 Wilcoxon single-rank test P-value: 3.56938820447e-08	554 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.768 Vsfold5: 0.368 Sensitivity PETfold_pre2.0(20): 0.677 Vsfold5: 0.343 Positive Predictive Value PETfold_pre2.0(20): 0.871 Vsfold5: 0.397 Number of pairs reference - predicted secondary structure: 554 Wilcoxon single-rank test P-value: 3.56938820447e-08	557 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.759 Vsfold5: 0.365 Sensitivity CentroidAlifold(20): 0.620 Vsfold5: 0.341 Positive Predictive Value CentroidAlifold(20): 0.929 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.674 Vsfold5: 0.339 Sensitivity CentroidHomfold‑LAST: 0.534 Vsfold5: 0.322 Positive Predictive Value CentroidHomfold‑LAST: 0.850 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	545 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.762 Vsfold5: 0.366 Sensitivity PPfold(20): 0.655 Vsfold5: 0.342 Positive Predictive Value PPfold(20): 0.887 Vsfold5: 0.395 Number of pairs reference - predicted secondary structure: 545 Wilcoxon single-rank test P-value: 3.56938820447e-08	557 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.708 Vsfold5: 0.365 Sensitivity RNAalifold(20): 0.580 Vsfold5: 0.341 Positive Predictive Value RNAalifold(20): 0.866 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	631 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.662 Vsfold5: 0.318 Sensitivity MXScarna(seed): 0.570 Vsfold5: 0.297 Positive Predictive Value MXScarna(seed): 0.770 Vsfold5: 0.343 Number of pairs reference - predicted secondary structure: 631 Wilcoxon single-rank test P-value: 3.56938820447e-08	557 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.701 Vsfold5: 0.365 Sensitivity MXScarna(20): 0.634 Vsfold5: 0.341 Positive Predictive Value MXScarna(20): 0.776 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.636 Vsfold5: 0.339 Sensitivity IPknot: 0.589 Vsfold5: 0.322 Positive Predictive Value IPknot: 0.689 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	527 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.686 Vsfold5: 0.377 Sensitivity Multilign(20): 0.618 Vsfold5: 0.351 Positive Predictive Value Multilign(20): 0.762 Vsfold5: 0.407 Number of pairs reference - predicted secondary structure: 527 Wilcoxon single-rank test P-value: 3.56938820447e-08	489 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.636 Vsfold5: 0.363 Sensitivity Murlet(20): 0.502 Vsfold5: 0.340 Positive Predictive Value Murlet(20): 0.807 Vsfold5: 0.390 Number of pairs reference - predicted secondary structure: 489 Wilcoxon single-rank test P-value: 3.56938820447e-08	599 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.550 Vsfold5: 0.312 Sensitivity RNAalifold(seed): 0.353 Vsfold5: 0.291 Positive Predictive Value RNAalifold(seed): 0.859 Vsfold5: 0.338 Number of pairs reference - predicted secondary structure: 599 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.600 Vsfold5: 0.339 Sensitivity CentroidFold: 0.553 Vsfold5: 0.322 Positive Predictive Value CentroidFold: 0.651 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.676 Vsfold5: 0.331 Sensitivity RNASampler(20): 0.522 Vsfold5: 0.315 Positive Predictive Value RNASampler(20): 0.877 Vsfold5: 0.352 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.587 Vsfold5: 0.339 Sensitivity Contrafold: 0.577 Vsfold5: 0.322 Positive Predictive Value Contrafold: 0.599 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.561 Vsfold5: 0.339 Sensitivity Sfold: 0.515 Vsfold5: 0.322 Positive Predictive Value Sfold: 0.613 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.681 Vsfold5: 0.271 Sensitivity Multilign(seed): 0.649 Vsfold5: 0.271 Positive Predictive Value Multilign(seed): 0.717 Vsfold5: 0.273 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	1602 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.563 Vsfold5: 0.339 Sensitivity MaxExpect: 0.551 Vsfold5: 0.322 Positive Predictive Value MaxExpect: 0.578 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.562 Vsfold5: 0.339 Sensitivity ProbKnot: 0.557 Vsfold5: 0.322 Positive Predictive Value ProbKnot: 0.568 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.545 Vsfold5: 0.339 Sensitivity Fold: 0.546 Vsfold5: 0.322 Positive Predictive Value Fold: 0.545 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.629 Vsfold5: 0.357 Sensitivity RNASampler(seed): 0.468 Vsfold5: 0.340 Positive Predictive Value RNASampler(seed): 0.847 Vsfold5: 0.379 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.532 Vsfold5: 0.339 Sensitivity UNAFold: 0.527 Vsfold5: 0.322 Positive Predictive Value UNAFold: 0.540 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.525 Vsfold5: 0.339 Sensitivity RNAsubopt: 0.530 Vsfold5: 0.322 Positive Predictive Value RNAsubopt: 0.521 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	557 RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.531 Vsfold5: 0.365 Sensitivity RSpredict(20): 0.393 Vsfold5: 0.341 Positive Predictive Value RSpredict(20): 0.719 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	553 CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.556 Vsfold5: 0.366 Sensitivity CMfinder(20): 0.388 Vsfold5: 0.342 Positive Predictive Value CMfinder(20): 0.799 Vsfold5: 0.395 Number of pairs reference - predicted secondary structure: 553 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.529 Vsfold5: 0.339 Sensitivity PknotsRG: 0.529 Vsfold5: 0.322 Positive Predictive Value PknotsRG: 0.531 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	557 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.472 Vsfold5: 0.365 Sensitivity Carnac(20): 0.251 Vsfold5: 0.341 Positive Predictive Value Carnac(20): 0.889 Vsfold5: 0.394 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.531 Vsfold5: 0.339 Sensitivity RNAfold: 0.530 Vsfold5: 0.322 Positive Predictive Value RNAfold: 0.533 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 CMfinder(seed) vs Vsfold5 Matthews Correlation Coefficient CMfinder(seed): 0.488 Vsfold5: 0.285 Sensitivity CMfinder(seed): 0.316 Vsfold5: 0.272 Positive Predictive Value CMfinder(seed): 0.755 Vsfold5: 0.301 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	971 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.539 Vsfold5: 0.335 Sensitivity Afold: 0.532 Vsfold5: 0.314 Positive Predictive Value Afold: 0.548 Vsfold5: 0.361 Number of pairs reference - predicted secondary structure: 971 Wilcoxon single-rank test P-value: 3.56938820447e-08	876 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.613 Vsfold5: 0.477 Sensitivity HotKnots: 0.607 Vsfold5: 0.450 Positive Predictive Value HotKnots: 0.624 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 876 Wilcoxon single-rank test P-value: 3.56938820447e-08	1601 CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.482 Vsfold5: 0.339 Sensitivity CRWrnafold: 0.482 Vsfold5: 0.322 Positive Predictive Value CRWrnafold: 0.484 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1601 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.606 Vsfold5: 0.579 Sensitivity Pknots: 0.595 Vsfold5: 0.548 Positive Predictive Value Pknots: 0.624 Vsfold5: 0.620 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.481 Vsfold5: 0.339 Sensitivity McQFold: 0.467 Vsfold5: 0.322 Positive Predictive Value McQFold: 0.496 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	1583 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.476 Vsfold5: 0.341 Sensitivity RNAshapes: 0.471 Vsfold5: 0.324 Positive Predictive Value RNAshapes: 0.483 Vsfold5: 0.361 Number of pairs reference - predicted secondary structure: 1583 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 PPfold(seed) vs Vsfold5 Matthews Correlation Coefficient PPfold(seed): 0.635 Vsfold5: 0.233 Sensitivity PPfold(seed): 0.511 Vsfold5: 0.221 Positive Predictive Value PPfold(seed): 0.790 Vsfold5: 0.250 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	557 Vsfold5 vs Mastr(20) Matthews Correlation Coefficient Vsfold5: 0.365 Mastr(20): 0.356 Sensitivity Vsfold5: 0.341 Mastr(20): 0.161 Positive Predictive Value Vsfold5: 0.394 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 557 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.519 Vsfold5: 0.278 Sensitivity Murlet(seed): 0.322 Vsfold5: 0.263 Positive Predictive Value Murlet(seed): 0.839 Vsfold5: 0.297 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	1542 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.471 Vsfold5: 0.342 Sensitivity RNASLOpt: 0.444 Vsfold5: 0.325 Positive Predictive Value RNASLOpt: 0.502 Vsfold5: 0.361 Number of pairs reference - predicted secondary structure: 1542 Wilcoxon single-rank test P-value: 3.56938820447e-08	798 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.575 Vsfold5: 0.497 Sensitivity Cylofold: 0.551 Vsfold5: 0.468 Positive Predictive Value Cylofold: 0.606 Vsfold5: 0.535 Number of pairs reference - predicted secondary structure: 798 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.387 Vsfold5: 0.339 Sensitivity RNAwolf: 0.401 Vsfold5: 0.322 Positive Predictive Value RNAwolf: 0.377 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08	1602 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.347 Vsfold5: 0.339 Sensitivity Vsfold4: 0.319 Vsfold5: 0.322 Positive Predictive Value Vsfold4: 0.379 Vsfold5: 0.359 Number of pairs reference - predicted secondary structure: 1602 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: 0.582 Alterna: 0.552 Sensitivity Vsfold5: 0.551 Alterna: 0.547 Positive Predictive Value Vsfold5: 0.623 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.582 RDfolder: 0.520 Sensitivity Vsfold5: 0.551 RDfolder: 0.464 Positive Predictive Value Vsfold5: 0.623 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.237 Carnac(seed): 0.234 Sensitivity Vsfold5: 0.225 Carnac(seed): 0.062 Positive Predictive Value Vsfold5: 0.252 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 244 Wilcoxon single-rank test P-value: 0.0155447020429	+ Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.489 MCFold: 0.473 Sensitivity Vsfold5: 0.460 MCFold: 0.524 Positive Predictive Value Vsfold5: 0.527 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.315 RSpredict(seed): 0.241 Sensitivity Vsfold5: 0.294 RSpredict(seed): 0.110 Positive Predictive Value Vsfold5: 0.340 RSpredict(seed): 0.534 Number of pairs reference - predicted secondary structure: 612 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.334 NanoFolder: 0.201 Sensitivity Vsfold5: 0.314 NanoFolder: 0.236 Positive Predictive Value Vsfold5: 0.358 NanoFolder: 0.174 Number of pairs reference - predicted secondary structure: 244 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.311 Mastr(seed): 0.120 Sensitivity Vsfold5: 0.292 Mastr(seed): 0.018 Positive Predictive Value Vsfold5: 0.335 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08
Alterna	24 TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): 0.720 Alterna: 0.546 Sensitivity TurboFold(seed): 0.663 Alterna: 0.520 Positive Predictive Value TurboFold(seed): 0.786 Alterna: 0.581 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.77766983502e-08	360 PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 Alterna: 0.585 Sensitivity PETfold_pre2.0(seed): 0.870 Alterna: 0.595 Positive Predictive Value PETfold_pre2.0(seed): 0.950 Alterna: 0.582 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.765 Alterna: 0.552 Sensitivity ContextFold: 0.723 Alterna: 0.547 Positive Predictive Value ContextFold: 0.814 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.913 Alterna: 0.618 Sensitivity TurboFold(20): 0.887 Alterna: 0.626 Positive Predictive Value TurboFold(20): 0.940 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.781 Alterna: 0.558 Sensitivity CentroidAlifold(seed): 0.674 Alterna: 0.548 Positive Predictive Value CentroidAlifold(seed): 0.908 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): 0.887 Alterna: 0.618 Sensitivity PETfold_pre2.0(20): 0.811 Alterna: 0.626 Positive Predictive Value PETfold_pre2.0(20): 0.973 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.907 Alterna: 0.618 Sensitivity CentroidAlifold(20): 0.844 Alterna: 0.626 Positive Predictive Value CentroidAlifold(20): 0.977 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.748 Alterna: 0.552 Sensitivity CentroidHomfold‑LAST: 0.687 Alterna: 0.547 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.884 Alterna: 0.618 Sensitivity PPfold(20): 0.800 Alterna: 0.626 Positive Predictive Value PPfold(20): 0.979 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.883 Alterna: 0.618 Sensitivity RNAalifold(20): 0.795 Alterna: 0.626 Positive Predictive Value RNAalifold(20): 0.982 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	156 MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.749 Alterna: 0.560 Sensitivity MXScarna(seed): 0.715 Alterna: 0.552 Positive Predictive Value MXScarna(seed): 0.788 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.873 Alterna: 0.618 Sensitivity MXScarna(20): 0.835 Alterna: 0.626 Positive Predictive Value MXScarna(20): 0.915 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.689 Alterna: 0.552 Sensitivity IPknot: 0.655 Alterna: 0.547 Positive Predictive Value IPknot: 0.731 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.829 Alterna: 0.616 Sensitivity Multilign(20): 0.758 Alterna: 0.624 Positive Predictive Value Multilign(20): 0.910 Alterna: 0.614 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.780 Alterna: 0.618 Sensitivity Murlet(20): 0.685 Alterna: 0.626 Positive Predictive Value Murlet(20): 0.892 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): 0.617 Alterna: 0.554 Sensitivity RNAalifold(seed): 0.418 Alterna: 0.541 Positive Predictive Value RNAalifold(seed): 0.917 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.658 Alterna: 0.552 Sensitivity CentroidFold: 0.621 Alterna: 0.547 Positive Predictive Value CentroidFold: 0.703 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.859 Alterna: 0.620 Sensitivity RNASampler(20): 0.761 Alterna: 0.627 Positive Predictive Value RNASampler(20): 0.971 Alterna: 0.618 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.657 Alterna: 0.552 Sensitivity Contrafold: 0.646 Alterna: 0.547 Positive Predictive Value Contrafold: 0.675 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.603 Alterna: 0.552 Sensitivity Sfold: 0.566 Alterna: 0.547 Positive Predictive Value Sfold: 0.649 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): 0.485 Alterna: 0.420 Sensitivity Multilign(seed): 0.386 Alterna: 0.391 Positive Predictive Value Multilign(seed): 0.619 Alterna: 0.462 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.64481516727e-08	693 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.641 Alterna: 0.552 Sensitivity MaxExpect: 0.622 Alterna: 0.547 Positive Predictive Value MaxExpect: 0.667 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.640 Alterna: 0.552 Sensitivity ProbKnot: 0.632 Alterna: 0.547 Positive Predictive Value ProbKnot: 0.656 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Fold vs Alterna Matthews Correlation Coefficient Fold: 0.633 Alterna: 0.552 Sensitivity Fold: 0.623 Alterna: 0.547 Positive Predictive Value Fold: 0.650 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): 0.455 Alterna: 0.449 Sensitivity RNASampler(seed): 0.284 Alterna: 0.422 Positive Predictive Value RNASampler(seed): 0.738 Alterna: 0.490 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 0.0716817872326	693 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.597 Alterna: 0.552 Sensitivity UNAFold: 0.584 Alterna: 0.547 Positive Predictive Value UNAFold: 0.617 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.608 Alterna: 0.552 Sensitivity RNAsubopt: 0.603 Alterna: 0.547 Positive Predictive Value RNAsubopt: 0.621 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.821 Alterna: 0.618 Sensitivity RSpredict(20): 0.738 Alterna: 0.626 Positive Predictive Value RSpredict(20): 0.917 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 CMfinder(20) vs Alterna Matthews Correlation Coefficient CMfinder(20): 0.792 Alterna: 0.618 Sensitivity CMfinder(20): 0.679 Alterna: 0.626 Positive Predictive Value CMfinder(20): 0.927 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.605 Alterna: 0.552 Sensitivity PknotsRG: 0.598 Alterna: 0.547 Positive Predictive Value PknotsRG: 0.619 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.744 Alterna: 0.618 Sensitivity Carnac(20): 0.591 Alterna: 0.626 Positive Predictive Value Carnac(20): 0.940 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.596 Alterna: 0.552 Sensitivity RNAfold: 0.589 Alterna: 0.547 Positive Predictive Value RNAfold: 0.611 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): 0.512 Alterna: 0.405 Sensitivity CMfinder(seed): 0.382 Alterna: 0.380 Positive Predictive Value CMfinder(seed): 0.696 Alterna: 0.445 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 Afold vs Alterna Matthews Correlation Coefficient Afold: 0.542 Alterna: 0.531 Sensitivity Afold: 0.522 Alterna: 0.509 Positive Predictive Value Afold: 0.574 Alterna: 0.565 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 4.48494289621e-08	693 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.594 Alterna: 0.552 Sensitivity HotKnots: 0.590 Alterna: 0.547 Positive Predictive Value HotKnots: 0.605 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	692 CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.615 Alterna: 0.552 Sensitivity CRWrnafold: 0.601 Alterna: 0.546 Positive Predictive Value CRWrnafold: 0.635 Alterna: 0.565 Number of pairs reference - predicted secondary structure: 692 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.610 Alterna: 0.552 Sensitivity Pknots: 0.599 Alterna: 0.547 Positive Predictive Value Pknots: 0.629 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.653 Alterna: 0.552 Sensitivity McQFold: 0.624 Alterna: 0.547 Positive Predictive Value McQFold: 0.689 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.596 Alterna: 0.552 Sensitivity RNAshapes: 0.587 Alterna: 0.547 Positive Predictive Value RNAshapes: 0.612 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.543 PPfold(seed): 0.501 Sensitivity Alterna: 0.529 PPfold(seed): 0.297 Positive Predictive Value Alterna: 0.565 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	211 Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.730 Alterna: 0.618 Sensitivity Mastr(20): 0.677 Alterna: 0.626 Positive Predictive Value Mastr(20): 0.790 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	71 Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.456 Murlet(seed): 0.451 Sensitivity Alterna: 0.430 Murlet(seed): 0.267 Positive Predictive Value Alterna: 0.494 Murlet(seed): 0.771 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 0.115804103359	693 RNASLOpt vs Alterna Matthews Correlation Coefficient RNASLOpt: 0.612 Alterna: 0.552 Sensitivity RNASLOpt: 0.567 Alterna: 0.547 Positive Predictive Value RNASLOpt: 0.667 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	673 Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.621 Alterna: 0.555 Sensitivity Cylofold: 0.599 Alterna: 0.549 Positive Predictive Value Cylofold: 0.650 Alterna: 0.569 Number of pairs reference - predicted secondary structure: 673 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: 0.552 RNAwolf: 0.551 Sensitivity Alterna: 0.547 RNAwolf: 0.555 Positive Predictive Value Alterna: 0.566 RNAwolf: 0.555 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 0.0853441262641	693 Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.596 Alterna: 0.552 Sensitivity Vsfold4: 0.547 Alterna: 0.547 Positive Predictive Value Vsfold4: 0.656 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: 0.582 Alterna: 0.552 Sensitivity Vsfold5: 0.551 Alterna: 0.547 Positive Predictive Value Vsfold5: 0.623 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.552 RDfolder: 0.520 Sensitivity Alterna: 0.547 RDfolder: 0.464 Positive Predictive Value Alterna: 0.566 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.507 Carnac(seed): 0.503 Sensitivity Alterna: 0.485 Carnac(seed): 0.281 Positive Predictive Value Alterna: 0.538 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 0.0617146490994	+ Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.552 MCFold: 0.468 Sensitivity Alterna: 0.543 MCFold: 0.524 Positive Predictive Value Alterna: 0.569 MCFold: 0.428 Number of pairs reference - predicted secondary structure: 649 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.558 RSpredict(seed): 0.472 Sensitivity Alterna: 0.548 RSpredict(seed): 0.337 Positive Predictive Value Alterna: 0.575 RSpredict(seed): 0.669 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.573 NanoFolder: 0.390 Sensitivity Alterna: 0.561 NanoFolder: 0.447 Positive Predictive Value Alterna: 0.593 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.560 Mastr(seed): 0.309 Sensitivity Alterna: 0.552 Mastr(seed): 0.118 Positive Predictive Value Alterna: 0.575 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08
RDfolder	24 TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.720 RDfolder: 0.512 Sensitivity TurboFold(seed): 0.663 RDfolder: 0.453 Positive Predictive Value TurboFold(seed): 0.786 RDfolder: 0.588 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	360 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 RDfolder: 0.557 Sensitivity PETfold_pre2.0(seed): 0.870 RDfolder: 0.511 Positive Predictive Value PETfold_pre2.0(seed): 0.950 RDfolder: 0.615 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.765 RDfolder: 0.520 Sensitivity ContextFold: 0.723 RDfolder: 0.464 Positive Predictive Value ContextFold: 0.814 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.913 RDfolder: 0.556 Sensitivity TurboFold(20): 0.887 RDfolder: 0.511 Positive Predictive Value TurboFold(20): 0.940 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.781 RDfolder: 0.468 Sensitivity CentroidAlifold(seed): 0.674 RDfolder: 0.402 Positive Predictive Value CentroidAlifold(seed): 0.908 RDfolder: 0.552 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.887 RDfolder: 0.556 Sensitivity PETfold_pre2.0(20): 0.811 RDfolder: 0.511 Positive Predictive Value PETfold_pre2.0(20): 0.973 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.907 RDfolder: 0.556 Sensitivity CentroidAlifold(20): 0.844 RDfolder: 0.511 Positive Predictive Value CentroidAlifold(20): 0.977 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.748 RDfolder: 0.520 Sensitivity CentroidHomfold‑LAST: 0.687 RDfolder: 0.464 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.884 RDfolder: 0.562 Sensitivity PPfold(20): 0.800 RDfolder: 0.517 Positive Predictive Value PPfold(20): 0.979 RDfolder: 0.618 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.883 RDfolder: 0.556 Sensitivity RNAalifold(20): 0.795 RDfolder: 0.511 Positive Predictive Value RNAalifold(20): 0.982 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	156 MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.749 RDfolder: 0.487 Sensitivity MXScarna(seed): 0.715 RDfolder: 0.421 Positive Predictive Value MXScarna(seed): 0.788 RDfolder: 0.571 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.873 RDfolder: 0.556 Sensitivity MXScarna(20): 0.835 RDfolder: 0.511 Positive Predictive Value MXScarna(20): 0.915 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.689 RDfolder: 0.520 Sensitivity IPknot: 0.655 RDfolder: 0.464 Positive Predictive Value IPknot: 0.731 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.829 RDfolder: 0.561 Sensitivity Multilign(20): 0.758 RDfolder: 0.517 Positive Predictive Value Multilign(20): 0.910 RDfolder: 0.616 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.780 RDfolder: 0.556 Sensitivity Murlet(20): 0.685 RDfolder: 0.511 Positive Predictive Value Murlet(20): 0.892 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.617 RDfolder: 0.448 Sensitivity RNAalifold(seed): 0.418 RDfolder: 0.382 Positive Predictive Value RNAalifold(seed): 0.917 RDfolder: 0.533 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.658 RDfolder: 0.520 Sensitivity CentroidFold: 0.621 RDfolder: 0.464 Positive Predictive Value CentroidFold: 0.703 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.859 RDfolder: 0.560 Sensitivity RNASampler(20): 0.761 RDfolder: 0.516 Positive Predictive Value RNASampler(20): 0.971 RDfolder: 0.614 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.657 RDfolder: 0.520 Sensitivity Contrafold: 0.646 RDfolder: 0.464 Positive Predictive Value Contrafold: 0.675 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.603 RDfolder: 0.520 Sensitivity Sfold: 0.566 RDfolder: 0.464 Positive Predictive Value Sfold: 0.649 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.485 RDfolder: 0.480 Sensitivity Multilign(seed): 0.386 RDfolder: 0.391 Positive Predictive Value Multilign(seed): 0.619 RDfolder: 0.600 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000665114514833	693 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.641 RDfolder: 0.520 Sensitivity MaxExpect: 0.622 RDfolder: 0.464 Positive Predictive Value MaxExpect: 0.667 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.640 RDfolder: 0.520 Sensitivity ProbKnot: 0.632 RDfolder: 0.464 Positive Predictive Value ProbKnot: 0.656 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.633 RDfolder: 0.520 Sensitivity Fold: 0.623 RDfolder: 0.464 Positive Predictive Value Fold: 0.650 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.455 RDfolder: 0.357 Sensitivity RNASampler(seed): 0.284 RDfolder: 0.288 Positive Predictive Value RNASampler(seed): 0.738 RDfolder: 0.456 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.597 RDfolder: 0.520 Sensitivity UNAFold: 0.584 RDfolder: 0.464 Positive Predictive Value UNAFold: 0.617 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.608 RDfolder: 0.520 Sensitivity RNAsubopt: 0.603 RDfolder: 0.464 Positive Predictive Value RNAsubopt: 0.621 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.821 RDfolder: 0.556 Sensitivity RSpredict(20): 0.738 RDfolder: 0.511 Positive Predictive Value RSpredict(20): 0.917 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.792 RDfolder: 0.556 Sensitivity CMfinder(20): 0.679 RDfolder: 0.511 Positive Predictive Value CMfinder(20): 0.927 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.605 RDfolder: 0.520 Sensitivity PknotsRG: 0.598 RDfolder: 0.464 Positive Predictive Value PknotsRG: 0.619 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.744 RDfolder: 0.556 Sensitivity Carnac(20): 0.591 RDfolder: 0.511 Positive Predictive Value Carnac(20): 0.940 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.596 RDfolder: 0.520 Sensitivity RNAfold: 0.589 RDfolder: 0.464 Positive Predictive Value RNAfold: 0.611 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 CMfinder(seed) vs RDfolder Matthews Correlation Coefficient CMfinder(seed): 0.512 RDfolder: 0.317 Sensitivity CMfinder(seed): 0.382 RDfolder: 0.254 Positive Predictive Value CMfinder(seed): 0.696 RDfolder: 0.411 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.542 RDfolder: 0.482 Sensitivity Afold: 0.522 RDfolder: 0.417 Positive Predictive Value Afold: 0.574 RDfolder: 0.569 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.594 RDfolder: 0.520 Sensitivity HotKnots: 0.590 RDfolder: 0.464 Positive Predictive Value HotKnots: 0.605 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	692 CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.615 RDfolder: 0.520 Sensitivity CRWrnafold: 0.601 RDfolder: 0.464 Positive Predictive Value CRWrnafold: 0.635 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 692 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.610 RDfolder: 0.520 Sensitivity Pknots: 0.599 RDfolder: 0.464 Positive Predictive Value Pknots: 0.629 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.653 RDfolder: 0.520 Sensitivity McQFold: 0.624 RDfolder: 0.464 Positive Predictive Value McQFold: 0.689 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.596 RDfolder: 0.520 Sensitivity RNAshapes: 0.587 RDfolder: 0.464 Positive Predictive Value RNAshapes: 0.612 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.528 PPfold(seed): 0.501 Sensitivity RDfolder: 0.462 PPfold(seed): 0.297 Positive Predictive Value RDfolder: 0.612 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.16498238667e-07	211 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.730 RDfolder: 0.556 Sensitivity Mastr(20): 0.677 RDfolder: 0.511 Positive Predictive Value Mastr(20): 0.790 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	71 Murlet(seed) vs RDfolder Matthews Correlation Coefficient Murlet(seed): 0.451 RDfolder: 0.361 Sensitivity Murlet(seed): 0.267 RDfolder: 0.294 Positive Predictive Value Murlet(seed): 0.771 RDfolder: 0.455 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.612 RDfolder: 0.520 Sensitivity RNASLOpt: 0.567 RDfolder: 0.464 Positive Predictive Value RNASLOpt: 0.667 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	673 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.621 RDfolder: 0.528 Sensitivity Cylofold: 0.599 RDfolder: 0.470 Positive Predictive Value Cylofold: 0.650 RDfolder: 0.601 Number of pairs reference - predicted secondary structure: 673 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.551 RDfolder: 0.520 Sensitivity RNAwolf: 0.555 RDfolder: 0.464 Positive Predictive Value RNAwolf: 0.555 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.596 RDfolder: 0.520 Sensitivity Vsfold4: 0.547 RDfolder: 0.464 Positive Predictive Value Vsfold4: 0.656 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.582 RDfolder: 0.520 Sensitivity Vsfold5: 0.551 RDfolder: 0.464 Positive Predictive Value Vsfold5: 0.623 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.552 RDfolder: 0.520 Sensitivity Alterna: 0.547 RDfolder: 0.464 Positive Predictive Value Alterna: 0.566 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Carnac(seed) vs RDfolder Matthews Correlation Coefficient Carnac(seed): 0.503 RDfolder: 0.434 Sensitivity Carnac(seed): 0.281 RDfolder: 0.361 Positive Predictive Value Carnac(seed): 0.907 RDfolder: 0.532 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.515 MCFold: 0.468 Sensitivity RDfolder: 0.457 MCFold: 0.524 Positive Predictive Value RDfolder: 0.589 MCFold: 0.428 Number of pairs reference - predicted secondary structure: 649 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RSpredict(seed) vs RDfolder Matthews Correlation Coefficient RSpredict(seed): 0.472 RDfolder: 0.468 Sensitivity RSpredict(seed): 0.337 RDfolder: 0.402 Positive Predictive Value RSpredict(seed): 0.669 RDfolder: 0.552 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 0.221270004692	+ RDfolder vs NanoFolder Matthews Correlation Coefficient RDfolder: 0.477 NanoFolder: 0.390 Sensitivity RDfolder: 0.419 NanoFolder: 0.447 Positive Predictive Value RDfolder: 0.550 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.485 Mastr(seed): 0.309 Sensitivity RDfolder: 0.420 Mastr(seed): 0.118 Positive Predictive Value RDfolder: 0.569 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08
Carnac(seed)	50 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.788 Carnac(seed): 0.431 Sensitivity TurboFold(seed): 0.760 Carnac(seed): 0.207 Positive Predictive Value TurboFold(seed): 0.819 Carnac(seed): 0.897 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	267 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.726 Carnac(seed): 0.245 Sensitivity PETfold_pre2.0(seed): 0.626 Carnac(seed): 0.069 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 267 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.735 Carnac(seed): 0.244 Sensitivity ContextFold: 0.710 Carnac(seed): 0.069 Positive Predictive Value ContextFold: 0.762 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	81 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.843 Carnac(seed): 0.310 Sensitivity TurboFold(20): 0.811 Carnac(seed): 0.106 Positive Predictive Value TurboFold(20): 0.877 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	266 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 Carnac(seed): 0.245 Sensitivity CentroidAlifold(seed): 0.599 Carnac(seed): 0.069 Positive Predictive Value CentroidAlifold(seed): 0.885 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 266 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.781 Carnac(seed): 0.398 Sensitivity PETfold_pre2.0(20): 0.680 Carnac(seed): 0.173 Positive Predictive Value PETfold_pre2.0(20): 0.898 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.819 Carnac(seed): 0.398 Sensitivity CentroidAlifold(20): 0.720 Carnac(seed): 0.173 Positive Predictive Value CentroidAlifold(20): 0.932 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.688 Carnac(seed): 0.224 Sensitivity CentroidHomfold‑LAST: 0.577 Carnac(seed): 0.057 Positive Predictive Value CentroidHomfold‑LAST: 0.821 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	80 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.732 Carnac(seed): 0.317 Sensitivity PPfold(20): 0.596 Carnac(seed): 0.111 Positive Predictive Value PPfold(20): 0.900 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.730 Carnac(seed): 0.398 Sensitivity RNAalifold(20): 0.600 Carnac(seed): 0.173 Positive Predictive Value RNAalifold(20): 0.889 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.665 Carnac(seed): 0.244 Sensitivity MXScarna(seed): 0.584 Carnac(seed): 0.069 Positive Predictive Value MXScarna(seed): 0.758 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.822 Carnac(seed): 0.398 Sensitivity MXScarna(20): 0.786 Carnac(seed): 0.173 Positive Predictive Value MXScarna(20): 0.860 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.644 Carnac(seed): 0.244 Sensitivity IPknot: 0.613 Carnac(seed): 0.069 Positive Predictive Value IPknot: 0.677 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.678 Carnac(seed): 0.357 Sensitivity Multilign(20): 0.562 Carnac(seed): 0.141 Positive Predictive Value Multilign(20): 0.820 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	79 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.640 Carnac(seed): 0.317 Sensitivity Murlet(20): 0.488 Carnac(seed): 0.111 Positive Predictive Value Murlet(20): 0.843 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 79 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.662 Carnac(seed): 0.246 Sensitivity RNAalifold(seed): 0.490 Carnac(seed): 0.070 Positive Predictive Value RNAalifold(seed): 0.896 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.624 Carnac(seed): 0.244 Sensitivity CentroidFold: 0.589 Carnac(seed): 0.069 Positive Predictive Value CentroidFold: 0.662 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.591 Carnac(seed): 0.338 Sensitivity RNASampler(20): 0.381 Carnac(seed): 0.127 Positive Predictive Value RNASampler(20): 0.920 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.614 Carnac(seed): 0.244 Sensitivity Contrafold: 0.610 Carnac(seed): 0.069 Positive Predictive Value Contrafold: 0.618 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.624 Carnac(seed): 0.244 Sensitivity Sfold: 0.583 Carnac(seed): 0.069 Positive Predictive Value Sfold: 0.668 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.698 Carnac(seed): 0.556 Sensitivity Multilign(seed): 0.660 Carnac(seed): 0.330 Positive Predictive Value Multilign(seed): 0.741 Carnac(seed): 0.940 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	269 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.583 Carnac(seed): 0.244 Sensitivity MaxExpect: 0.579 Carnac(seed): 0.069 Positive Predictive Value MaxExpect: 0.588 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.578 Carnac(seed): 0.244 Sensitivity ProbKnot: 0.579 Carnac(seed): 0.069 Positive Predictive Value ProbKnot: 0.579 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.572 Carnac(seed): 0.244 Sensitivity Fold: 0.579 Carnac(seed): 0.069 Positive Predictive Value Fold: 0.567 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.629 Carnac(seed): 0.520 Sensitivity RNASampler(seed): 0.468 Carnac(seed): 0.310 Positive Predictive Value RNASampler(seed): 0.847 Carnac(seed): 0.874 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.593 Carnac(seed): 0.244 Sensitivity UNAFold: 0.590 Carnac(seed): 0.069 Positive Predictive Value UNAFold: 0.597 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.570 Carnac(seed): 0.224 Sensitivity RNAsubopt: 0.577 Carnac(seed): 0.057 Positive Predictive Value RNAsubopt: 0.564 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.744 Carnac(seed): 0.398 Sensitivity RSpredict(20): 0.655 Carnac(seed): 0.173 Positive Predictive Value RSpredict(20): 0.846 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	81 CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.599 Carnac(seed): 0.310 Sensitivity CMfinder(20): 0.453 Carnac(seed): 0.106 Positive Predictive Value CMfinder(20): 0.794 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.589 Carnac(seed): 0.244 Sensitivity PknotsRG: 0.593 Carnac(seed): 0.069 Positive Predictive Value PknotsRG: 0.586 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.531 Carnac(seed): 0.398 Sensitivity Carnac(20): 0.310 Carnac(seed): 0.173 Positive Predictive Value Carnac(20): 0.913 Carnac(seed): 0.918 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	269 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.586 Carnac(seed): 0.244 Sensitivity RNAfold: 0.588 Carnac(seed): 0.069 Positive Predictive Value RNAfold: 0.585 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 269 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): 0.486 Carnac(seed): 0.306 Sensitivity CMfinder(seed): 0.314 Carnac(seed): 0.110 Positive Predictive Value CMfinder(seed): 0.755 Carnac(seed): 0.857 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	227 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.575 Carnac(seed): 0.258 Sensitivity Afold: 0.577 Carnac(seed): 0.076 Positive Predictive Value Afold: 0.574 Carnac(seed): 0.880 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.619 Carnac(seed): 0.414 Sensitivity HotKnots: 0.615 Carnac(seed): 0.197 Positive Predictive Value HotKnots: 0.629 Carnac(seed): 0.875 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	268 CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.504 Carnac(seed): 0.215 Sensitivity CRWrnafold: 0.507 Carnac(seed): 0.055 Positive Predictive Value CRWrnafold: 0.503 Carnac(seed): 0.850 Number of pairs reference - predicted secondary structure: 268 Wilcoxon single-rank test P-value: 3.56938820447e-08	90 Carnac(seed) vs Pknots Matthews Correlation Coefficient Carnac(seed): 0.498 Pknots: 0.484 Sensitivity Carnac(seed): 0.276 Pknots: 0.470 Positive Predictive Value Carnac(seed): 0.907 Pknots: 0.509 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 0.000186465496926	268 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.454 Carnac(seed): 0.215 Sensitivity McQFold: 0.444 Carnac(seed): 0.055 Positive Predictive Value McQFold: 0.467 Carnac(seed): 0.850 Number of pairs reference - predicted secondary structure: 268 Wilcoxon single-rank test P-value: 3.56938820447e-08	241 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.544 Carnac(seed): 0.228 Sensitivity RNAshapes: 0.539 Carnac(seed): 0.059 Positive Predictive Value RNAshapes: 0.551 Carnac(seed): 0.881 Number of pairs reference - predicted secondary structure: 241 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.631 Carnac(seed): 0.369 Sensitivity PPfold(seed): 0.502 Carnac(seed): 0.153 Positive Predictive Value PPfold(seed): 0.794 Carnac(seed): 0.896 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	81 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.532 Carnac(seed): 0.310 Sensitivity Mastr(20): 0.327 Carnac(seed): 0.106 Positive Predictive Value Mastr(20): 0.870 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	122 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.530 Carnac(seed): 0.384 Sensitivity Murlet(seed): 0.336 Carnac(seed): 0.174 Positive Predictive Value Murlet(seed): 0.839 Carnac(seed): 0.850 Number of pairs reference - predicted secondary structure: 122 Wilcoxon single-rank test P-value: 3.56938820447e-08	239 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.452 Carnac(seed): 0.240 Sensitivity RNASLOpt: 0.424 Carnac(seed): 0.065 Positive Predictive Value RNASLOpt: 0.484 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 239 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.541 Carnac(seed): 0.408 Sensitivity Cylofold: 0.502 Carnac(seed): 0.189 Positive Predictive Value Cylofold: 0.591 Carnac(seed): 0.888 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	268 RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.369 Carnac(seed): 0.215 Sensitivity RNAwolf: 0.382 Carnac(seed): 0.055 Positive Predictive Value RNAwolf: 0.358 Carnac(seed): 0.850 Number of pairs reference - predicted secondary structure: 268 Wilcoxon single-rank test P-value: 3.56938820447e-08	247 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.251 Carnac(seed): 0.231 Sensitivity Vsfold4: 0.231 Carnac(seed): 0.061 Positive Predictive Value Vsfold4: 0.277 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 247 Wilcoxon single-rank test P-value: 3.56938820447e-08	244 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.237 Carnac(seed): 0.234 Sensitivity Vsfold5: 0.225 Carnac(seed): 0.062 Positive Predictive Value Vsfold5: 0.252 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 244 Wilcoxon single-rank test P-value: 0.0155447020429	89 Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.507 Carnac(seed): 0.503 Sensitivity Alterna: 0.485 Carnac(seed): 0.281 Positive Predictive Value Alterna: 0.538 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 0.0617146490994	89 Carnac(seed) vs RDfolder Matthews Correlation Coefficient Carnac(seed): 0.503 RDfolder: 0.434 Sensitivity Carnac(seed): 0.281 RDfolder: 0.361 Positive Predictive Value Carnac(seed): 0.907 RDfolder: 0.532 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08		= MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.446 Carnac(seed): 0.444 Sensitivity MCFold: 0.494 Carnac(seed): 0.222 Positive Predictive Value MCFold: 0.411 Carnac(seed): 0.896 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 0.00636070127375	- RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.352 Carnac(seed): 0.245 Sensitivity RSpredict(seed): 0.202 Carnac(seed): 0.069 Positive Predictive Value RSpredict(seed): 0.614 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 266 Wilcoxon single-rank test P-value: 3.56938820447e-08	= NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.260 Carnac(seed): 0.257 Sensitivity NanoFolder: 0.303 Carnac(seed): 0.073 Positive Predictive Value NanoFolder: 0.226 Carnac(seed): 0.911 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.339915559821	+ Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.215 Mastr(seed): 0.192 Sensitivity Carnac(seed): 0.055 Mastr(seed): 0.045 Positive Predictive Value Carnac(seed): 0.850 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 268 Wilcoxon single-rank test P-value: 3.56938820447e-08
MCFold	30 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.788 MCFold: 0.459 Sensitivity TurboFold(seed): 0.752 MCFold: 0.515 Positive Predictive Value TurboFold(seed): 0.828 MCFold: 0.417 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	407 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.880 MCFold: 0.480 Sensitivity PETfold_pre2.0(seed): 0.828 MCFold: 0.542 Positive Predictive Value PETfold_pre2.0(seed): 0.938 MCFold: 0.431 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.771 MCFold: 0.473 Sensitivity ContextFold: 0.731 MCFold: 0.524 Positive Predictive Value ContextFold: 0.817 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.885 MCFold: 0.500 Sensitivity TurboFold(20): 0.859 MCFold: 0.559 Positive Predictive Value TurboFold(20): 0.914 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	185 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.786 MCFold: 0.472 Sensitivity CentroidAlifold(seed): 0.691 MCFold: 0.523 Positive Predictive Value CentroidAlifold(seed): 0.896 MCFold: 0.432 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.838 MCFold: 0.500 Sensitivity PETfold_pre2.0(20): 0.724 MCFold: 0.559 Positive Predictive Value PETfold_pre2.0(20): 0.973 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.840 MCFold: 0.500 Sensitivity CentroidAlifold(20): 0.742 MCFold: 0.559 Positive Predictive Value CentroidAlifold(20): 0.953 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 MCFold: 0.473 Sensitivity CentroidHomfold‑LAST: 0.671 MCFold: 0.524 Positive Predictive Value CentroidHomfold‑LAST: 0.812 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	254 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.830 MCFold: 0.500 Sensitivity PPfold(20): 0.707 MCFold: 0.560 Positive Predictive Value PPfold(20): 0.976 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.817 MCFold: 0.500 Sensitivity RNAalifold(20): 0.689 MCFold: 0.559 Positive Predictive Value RNAalifold(20): 0.970 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	198 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.752 MCFold: 0.472 Sensitivity MXScarna(seed): 0.715 MCFold: 0.525 Positive Predictive Value MXScarna(seed): 0.793 MCFold: 0.432 Number of pairs reference - predicted secondary structure: 198 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.833 MCFold: 0.500 Sensitivity MXScarna(20): 0.786 MCFold: 0.559 Positive Predictive Value MXScarna(20): 0.886 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.689 MCFold: 0.473 Sensitivity IPknot: 0.654 MCFold: 0.524 Positive Predictive Value IPknot: 0.730 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.774 MCFold: 0.498 Sensitivity Multilign(20): 0.681 MCFold: 0.558 Positive Predictive Value Multilign(20): 0.883 MCFold: 0.451 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	257 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.748 MCFold: 0.501 Sensitivity Murlet(20): 0.616 MCFold: 0.560 Positive Predictive Value Murlet(20): 0.911 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 257 Wilcoxon single-rank test P-value: 3.56938820447e-08	175 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.612 MCFold: 0.476 Sensitivity RNAalifold(seed): 0.404 MCFold: 0.525 Positive Predictive Value RNAalifold(seed): 0.932 MCFold: 0.438 Number of pairs reference - predicted secondary structure: 175 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.655 MCFold: 0.473 Sensitivity CentroidFold: 0.618 MCFold: 0.524 Positive Predictive Value CentroidFold: 0.699 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	254 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.771 MCFold: 0.500 Sensitivity RNASampler(20): 0.623 MCFold: 0.560 Positive Predictive Value RNASampler(20): 0.956 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.654 MCFold: 0.473 Sensitivity Contrafold: 0.642 MCFold: 0.524 Positive Predictive Value Contrafold: 0.672 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.621 MCFold: 0.473 Sensitivity Sfold: 0.583 MCFold: 0.524 Positive Predictive Value Sfold: 0.668 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.485 MCFold: 0.359 Sensitivity Multilign(seed): 0.386 MCFold: 0.419 Positive Predictive Value Multilign(seed): 0.619 MCFold: 0.319 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.53777893337e-08	761 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.642 MCFold: 0.473 Sensitivity MaxExpect: 0.623 MCFold: 0.524 Positive Predictive Value MaxExpect: 0.666 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.639 MCFold: 0.473 Sensitivity ProbKnot: 0.628 MCFold: 0.524 Positive Predictive Value ProbKnot: 0.656 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 Fold vs MCFold Matthews Correlation Coefficient Fold: 0.635 MCFold: 0.473 Sensitivity Fold: 0.625 MCFold: 0.524 Positive Predictive Value Fold: 0.651 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.502 MCFold: 0.422 Sensitivity RNASampler(seed): 0.334 MCFold: 0.464 Positive Predictive Value RNASampler(seed): 0.760 MCFold: 0.391 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.618 MCFold: 0.473 Sensitivity UNAFold: 0.601 MCFold: 0.524 Positive Predictive Value UNAFold: 0.640 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.619 MCFold: 0.473 Sensitivity RNAsubopt: 0.610 MCFold: 0.524 Positive Predictive Value RNAsubopt: 0.633 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.789 MCFold: 0.500 Sensitivity RSpredict(20): 0.690 MCFold: 0.559 Positive Predictive Value RSpredict(20): 0.905 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	254 CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.738 MCFold: 0.498 Sensitivity CMfinder(20): 0.608 MCFold: 0.558 Positive Predictive Value CMfinder(20): 0.898 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.620 MCFold: 0.473 Sensitivity PknotsRG: 0.610 MCFold: 0.524 Positive Predictive Value PknotsRG: 0.635 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.677 MCFold: 0.500 Sensitivity Carnac(20): 0.505 MCFold: 0.559 Positive Predictive Value Carnac(20): 0.912 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.615 MCFold: 0.473 Sensitivity RNAfold: 0.604 MCFold: 0.524 Positive Predictive Value RNAfold: 0.632 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): 0.555 MCFold: 0.396 Sensitivity CMfinder(seed): 0.421 MCFold: 0.436 Positive Predictive Value CMfinder(seed): 0.736 MCFold: 0.367 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	472 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.556 MCFold: 0.482 Sensitivity Afold: 0.538 MCFold: 0.521 Positive Predictive Value Afold: 0.581 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 472 Wilcoxon single-rank test P-value: 3.56938820447e-08	760 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.614 MCFold: 0.473 Sensitivity HotKnots: 0.606 MCFold: 0.524 Positive Predictive Value HotKnots: 0.627 MCFold: 0.434 Number of pairs reference - predicted secondary structure: 760 Wilcoxon single-rank test P-value: 3.56938820447e-08	760 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.629 MCFold: 0.473 Sensitivity CRWrnafold: 0.614 MCFold: 0.524 Positive Predictive Value CRWrnafold: 0.649 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 760 Wilcoxon single-rank test P-value: 3.56938820447e-08	653 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.598 MCFold: 0.466 Sensitivity Pknots: 0.585 MCFold: 0.521 Positive Predictive Value Pknots: 0.620 MCFold: 0.426 Number of pairs reference - predicted secondary structure: 653 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.593 MCFold: 0.473 Sensitivity McQFold: 0.563 MCFold: 0.524 Positive Predictive Value McQFold: 0.631 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.617 MCFold: 0.473 Sensitivity RNAshapes: 0.605 MCFold: 0.524 Positive Predictive Value RNAshapes: 0.635 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.421 PPfold(seed): 0.417 Sensitivity MCFold: 0.478 PPfold(seed): 0.206 Positive Predictive Value MCFold: 0.378 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 0.135703339508	258 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.710 MCFold: 0.500 Sensitivity Mastr(20): 0.637 MCFold: 0.559 Positive Predictive Value Mastr(20): 0.796 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.431 MCFold: 0.427 Sensitivity Murlet(seed): 0.236 MCFold: 0.470 Positive Predictive Value Murlet(seed): 0.793 MCFold: 0.396 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 0.397105643544	761 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.577 MCFold: 0.473 Sensitivity RNASLOpt: 0.531 MCFold: 0.524 Positive Predictive Value RNASLOpt: 0.633 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	714 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.584 MCFold: 0.487 Sensitivity Cylofold: 0.559 MCFold: 0.542 Positive Predictive Value Cylofold: 0.617 MCFold: 0.447 Number of pairs reference - predicted secondary structure: 714 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: 0.530 MCFold: 0.473 Sensitivity RNAwolf: 0.532 MCFold: 0.524 Positive Predictive Value RNAwolf: 0.534 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.500 MCFold: 0.473 Sensitivity Vsfold4: 0.456 MCFold: 0.524 Positive Predictive Value Vsfold4: 0.555 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.489 MCFold: 0.473 Sensitivity Vsfold5: 0.460 MCFold: 0.524 Positive Predictive Value Vsfold5: 0.527 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	649 Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.552 MCFold: 0.468 Sensitivity Alterna: 0.543 MCFold: 0.524 Positive Predictive Value Alterna: 0.569 MCFold: 0.428 Number of pairs reference - predicted secondary structure: 649 Wilcoxon single-rank test P-value: 3.56938820447e-08	649 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.515 MCFold: 0.468 Sensitivity RDfolder: 0.457 MCFold: 0.524 Positive Predictive Value RDfolder: 0.589 MCFold: 0.428 Number of pairs reference - predicted secondary structure: 649 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.446 Carnac(seed): 0.444 Sensitivity MCFold: 0.494 Carnac(seed): 0.222 Positive Predictive Value MCFold: 0.411 Carnac(seed): 0.896 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 0.00636070127375		+ MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.472 RSpredict(seed): 0.391 Sensitivity MCFold: 0.523 RSpredict(seed): 0.265 Positive Predictive Value MCFold: 0.432 RSpredict(seed): 0.583 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.456 NanoFolder: 0.352 Sensitivity MCFold: 0.509 NanoFolder: 0.404 Positive Predictive Value MCFold: 0.416 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.473 Mastr(seed): 0.261 Sensitivity MCFold: 0.525 Mastr(seed): 0.084 Positive Predictive Value MCFold: 0.433 Mastr(seed): 0.822 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08
RSpredict(seed)	50 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.788 RSpredict(seed): 0.495 Sensitivity TurboFold(seed): 0.760 RSpredict(seed): 0.378 Positive Predictive Value TurboFold(seed): 0.819 RSpredict(seed): 0.650 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	684 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.763 RSpredict(seed): 0.364 Sensitivity PETfold_pre2.0(seed): 0.698 RSpredict(seed): 0.224 Positive Predictive Value PETfold_pre2.0(seed): 0.835 RSpredict(seed): 0.594 Number of pairs reference - predicted secondary structure: 684 Wilcoxon single-rank test P-value: 3.56938820447e-08	702 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.811 RSpredict(seed): 0.369 Sensitivity ContextFold: 0.772 RSpredict(seed): 0.229 Positive Predictive Value ContextFold: 0.851 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	346 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.779 RSpredict(seed): 0.238 Sensitivity TurboFold(20): 0.731 RSpredict(seed): 0.104 Positive Predictive Value TurboFold(20): 0.831 RSpredict(seed): 0.546 Number of pairs reference - predicted secondary structure: 346 Wilcoxon single-rank test P-value: 3.56938820447e-08	699 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.748 RSpredict(seed): 0.370 Sensitivity CentroidAlifold(seed): 0.620 RSpredict(seed): 0.230 Positive Predictive Value CentroidAlifold(seed): 0.902 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 699 Wilcoxon single-rank test P-value: 3.56938820447e-08	395 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.762 RSpredict(seed): 0.410 Sensitivity PETfold_pre2.0(20): 0.697 RSpredict(seed): 0.276 Positive Predictive Value PETfold_pre2.0(20): 0.834 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 395 Wilcoxon single-rank test P-value: 3.56938820447e-08	398 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.757 RSpredict(seed): 0.410 Sensitivity CentroidAlifold(20): 0.631 RSpredict(seed): 0.277 Positive Predictive Value CentroidAlifold(20): 0.910 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	632 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.699 RSpredict(seed): 0.236 Sensitivity CentroidHomfold‑LAST: 0.561 RSpredict(seed): 0.105 Positive Predictive Value CentroidHomfold‑LAST: 0.872 RSpredict(seed): 0.530 Number of pairs reference - predicted secondary structure: 632 Wilcoxon single-rank test P-value: 3.56938820447e-08	337 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.740 RSpredict(seed): 0.288 Sensitivity PPfold(20): 0.627 RSpredict(seed): 0.140 Positive Predictive Value PPfold(20): 0.874 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 337 Wilcoxon single-rank test P-value: 3.56938820447e-08	398 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.710 RSpredict(seed): 0.410 Sensitivity RNAalifold(20): 0.613 RSpredict(seed): 0.277 Positive Predictive Value RNAalifold(20): 0.823 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	701 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.653 RSpredict(seed): 0.370 Sensitivity MXScarna(seed): 0.567 RSpredict(seed): 0.229 Positive Predictive Value MXScarna(seed): 0.753 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 701 Wilcoxon single-rank test P-value: 3.56938820447e-08	398 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.668 RSpredict(seed): 0.410 Sensitivity MXScarna(20): 0.600 RSpredict(seed): 0.277 Positive Predictive Value MXScarna(20): 0.744 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	702 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.632 RSpredict(seed): 0.369 Sensitivity IPknot: 0.571 RSpredict(seed): 0.229 Positive Predictive Value IPknot: 0.700 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	318 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.650 RSpredict(seed): 0.233 Sensitivity Multilign(20): 0.574 RSpredict(seed): 0.099 Positive Predictive Value Multilign(20): 0.737 RSpredict(seed): 0.548 Number of pairs reference - predicted secondary structure: 318 Wilcoxon single-rank test P-value: 3.56938820447e-08	284 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.585 RSpredict(seed): 0.300 Sensitivity Murlet(20): 0.446 RSpredict(seed): 0.161 Positive Predictive Value Murlet(20): 0.769 RSpredict(seed): 0.560 Number of pairs reference - predicted secondary structure: 284 Wilcoxon single-rank test P-value: 3.56938820447e-08	689 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.634 RSpredict(seed): 0.371 Sensitivity RNAalifold(seed): 0.476 RSpredict(seed): 0.230 Positive Predictive Value RNAalifold(seed): 0.844 RSpredict(seed): 0.598 Number of pairs reference - predicted secondary structure: 689 Wilcoxon single-rank test P-value: 3.56938820447e-08	701 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.600 RSpredict(seed): 0.373 Sensitivity CentroidFold: 0.540 RSpredict(seed): 0.231 Positive Predictive Value CentroidFold: 0.667 RSpredict(seed): 0.605 Number of pairs reference - predicted secondary structure: 701 Wilcoxon single-rank test P-value: 3.56938820447e-08	178 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.590 RSpredict(seed): 0.444 Sensitivity RNASampler(20): 0.389 RSpredict(seed): 0.303 Positive Predictive Value RNASampler(20): 0.898 RSpredict(seed): 0.653 Number of pairs reference - predicted secondary structure: 178 Wilcoxon single-rank test P-value: 3.56938820447e-08	702 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.585 RSpredict(seed): 0.369 Sensitivity Contrafold: 0.567 RSpredict(seed): 0.229 Positive Predictive Value Contrafold: 0.605 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	702 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.571 RSpredict(seed): 0.369 Sensitivity Sfold: 0.516 RSpredict(seed): 0.229 Positive Predictive Value Sfold: 0.633 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.698 RSpredict(seed): 0.586 Sensitivity Multilign(seed): 0.660 RSpredict(seed): 0.477 Positive Predictive Value Multilign(seed): 0.741 RSpredict(seed): 0.722 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	702 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.547 RSpredict(seed): 0.369 Sensitivity MaxExpect: 0.532 RSpredict(seed): 0.229 Positive Predictive Value MaxExpect: 0.563 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	702 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.544 RSpredict(seed): 0.369 Sensitivity ProbKnot: 0.533 RSpredict(seed): 0.229 Positive Predictive Value ProbKnot: 0.555 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	702 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.522 RSpredict(seed): 0.369 Sensitivity Fold: 0.521 RSpredict(seed): 0.229 Positive Predictive Value Fold: 0.524 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.629 RSpredict(seed): 0.607 Sensitivity RNASampler(seed): 0.468 RSpredict(seed): 0.495 Positive Predictive Value RNASampler(seed): 0.847 RSpredict(seed): 0.747 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	702 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.539 RSpredict(seed): 0.369 Sensitivity UNAFold: 0.530 RSpredict(seed): 0.229 Positive Predictive Value UNAFold: 0.548 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	632 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.570 RSpredict(seed): 0.236 Sensitivity RNAsubopt: 0.571 RSpredict(seed): 0.105 Positive Predictive Value RNAsubopt: 0.570 RSpredict(seed): 0.530 Number of pairs reference - predicted secondary structure: 632 Wilcoxon single-rank test P-value: 3.56938820447e-08	398 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.524 RSpredict(seed): 0.410 Sensitivity RSpredict(20): 0.416 RSpredict(seed): 0.277 Positive Predictive Value RSpredict(20): 0.661 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	342 CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.520 RSpredict(seed): 0.239 Sensitivity CMfinder(20): 0.351 RSpredict(seed): 0.105 Positive Predictive Value CMfinder(20): 0.773 RSpredict(seed): 0.550 Number of pairs reference - predicted secondary structure: 342 Wilcoxon single-rank test P-value: 3.56938820447e-08	690 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.534 RSpredict(seed): 0.395 Sensitivity PknotsRG: 0.529 RSpredict(seed): 0.238 Positive Predictive Value PknotsRG: 0.541 RSpredict(seed): 0.656 Number of pairs reference - predicted secondary structure: 690 Wilcoxon single-rank test P-value: 3.56938820447e-08	398 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.501 RSpredict(seed): 0.410 Sensitivity Carnac(20): 0.278 RSpredict(seed): 0.277 Positive Predictive Value Carnac(20): 0.904 RSpredict(seed): 0.609 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	702 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.524 RSpredict(seed): 0.369 Sensitivity RNAfold: 0.519 RSpredict(seed): 0.229 Positive Predictive Value RNAfold: 0.529 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 CMfinder(seed) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(seed): 0.486 RSpredict(seed): 0.484 Sensitivity CMfinder(seed): 0.312 RSpredict(seed): 0.331 Positive Predictive Value CMfinder(seed): 0.757 RSpredict(seed): 0.709 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 0.375011270663	572 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.517 RSpredict(seed): 0.386 Sensitivity Afold: 0.511 RSpredict(seed): 0.244 Positive Predictive Value Afold: 0.524 RSpredict(seed): 0.612 Number of pairs reference - predicted secondary structure: 572 Wilcoxon single-rank test P-value: 3.56938820447e-08	213 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.687 RSpredict(seed): 0.379 Sensitivity HotKnots: 0.688 RSpredict(seed): 0.256 Positive Predictive Value HotKnots: 0.691 RSpredict(seed): 0.569 Number of pairs reference - predicted secondary structure: 213 Wilcoxon single-rank test P-value: 3.56938820447e-08	670 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.509 RSpredict(seed): 0.341 Sensitivity CRWrnafold: 0.504 RSpredict(seed): 0.188 Positive Predictive Value CRWrnafold: 0.516 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 670 Wilcoxon single-rank test P-value: 3.56938820447e-08	146 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.509 RSpredict(seed): 0.475 Sensitivity Pknots: 0.504 RSpredict(seed): 0.341 Positive Predictive Value Pknots: 0.523 RSpredict(seed): 0.669 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	645 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.475 RSpredict(seed): 0.237 Sensitivity McQFold: 0.458 RSpredict(seed): 0.107 Positive Predictive Value McQFold: 0.495 RSpredict(seed): 0.528 Number of pairs reference - predicted secondary structure: 645 Wilcoxon single-rank test P-value: 3.56938820447e-08	607 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.527 RSpredict(seed): 0.240 Sensitivity RNAshapes: 0.516 RSpredict(seed): 0.109 Positive Predictive Value RNAshapes: 0.540 RSpredict(seed): 0.533 Number of pairs reference - predicted secondary structure: 607 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.626 RSpredict(seed): 0.398 Sensitivity PPfold(seed): 0.495 RSpredict(seed): 0.277 Positive Predictive Value PPfold(seed): 0.794 RSpredict(seed): 0.574 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	354 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.225 RSpredict(seed): 0.179 Sensitivity Mastr(20): 0.061 RSpredict(seed): 0.090 Positive Predictive Value Mastr(20): 0.827 RSpredict(seed): 0.358 Number of pairs reference - predicted secondary structure: 354 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.540 RSpredict(seed): 0.519 Sensitivity Murlet(seed): 0.360 RSpredict(seed): 0.395 Positive Predictive Value Murlet(seed): 0.811 RSpredict(seed): 0.682 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 4.48494289621e-08	584 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.479 RSpredict(seed): 0.253 Sensitivity RNASLOpt: 0.446 RSpredict(seed): 0.118 Positive Predictive Value RNASLOpt: 0.517 RSpredict(seed): 0.544 Number of pairs reference - predicted secondary structure: 584 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.518 RSpredict(seed): 0.402 Sensitivity Cylofold: 0.491 RSpredict(seed): 0.279 Positive Predictive Value Cylofold: 0.552 RSpredict(seed): 0.588 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	645 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.394 RSpredict(seed): 0.237 Sensitivity RNAwolf: 0.404 RSpredict(seed): 0.107 Positive Predictive Value RNAwolf: 0.387 RSpredict(seed): 0.528 Number of pairs reference - predicted secondary structure: 645 Wilcoxon single-rank test P-value: 3.56938820447e-08	617 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.339 RSpredict(seed): 0.241 Sensitivity Vsfold4: 0.307 RSpredict(seed): 0.109 Positive Predictive Value Vsfold4: 0.376 RSpredict(seed): 0.533 Number of pairs reference - predicted secondary structure: 617 Wilcoxon single-rank test P-value: 3.56938820447e-08	612 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.315 RSpredict(seed): 0.241 Sensitivity Vsfold5: 0.294 RSpredict(seed): 0.110 Positive Predictive Value Vsfold5: 0.340 RSpredict(seed): 0.534 Number of pairs reference - predicted secondary structure: 612 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.558 RSpredict(seed): 0.472 Sensitivity Alterna: 0.548 RSpredict(seed): 0.337 Positive Predictive Value Alterna: 0.575 RSpredict(seed): 0.669 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 RSpredict(seed) vs RDfolder Matthews Correlation Coefficient RSpredict(seed): 0.472 RDfolder: 0.468 Sensitivity RSpredict(seed): 0.337 RDfolder: 0.402 Positive Predictive Value RSpredict(seed): 0.669 RDfolder: 0.552 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 0.221270004692	266 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.352 Carnac(seed): 0.245 Sensitivity RSpredict(seed): 0.202 Carnac(seed): 0.069 Positive Predictive Value RSpredict(seed): 0.614 Carnac(seed): 0.867 Number of pairs reference - predicted secondary structure: 266 Wilcoxon single-rank test P-value: 3.56938820447e-08	185 MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.472 RSpredict(seed): 0.391 Sensitivity MCFold: 0.523 RSpredict(seed): 0.265 Positive Predictive Value MCFold: 0.432 RSpredict(seed): 0.583 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RSpredict(seed) vs NanoFolder Matthews Correlation Coefficient RSpredict(seed): 0.236 NanoFolder: 0.201 Sensitivity RSpredict(seed): 0.105 NanoFolder: 0.231 Positive Predictive Value RSpredict(seed): 0.535 NanoFolder: 0.178 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.235 Mastr(seed): 0.115 Sensitivity RSpredict(seed): 0.111 Mastr(seed): 0.016 Positive Predictive Value RSpredict(seed): 0.500 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 620 Wilcoxon single-rank test P-value: 3.56938820447e-08
NanoFolder	13 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.834 NanoFolder: 0.297 Sensitivity TurboFold(seed): 0.797 NanoFolder: 0.355 Positive Predictive Value TurboFold(seed): 0.874 NanoFolder: 0.254 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.39551335374e-08	188 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.742 NanoFolder: 0.201 Sensitivity PETfold_pre2.0(seed): 0.655 NanoFolder: 0.237 Positive Predictive Value PETfold_pre2.0(seed): 0.841 NanoFolder: 0.173 Number of pairs reference - predicted secondary structure: 188 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.788 NanoFolder: 0.194 Sensitivity ContextFold: 0.749 NanoFolder: 0.229 Positive Predictive Value ContextFold: 0.831 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.768 NanoFolder: 0.189 Sensitivity TurboFold(20): 0.720 NanoFolder: 0.218 Positive Predictive Value TurboFold(20): 0.820 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.732 NanoFolder: 0.201 Sensitivity CentroidAlifold(seed): 0.580 NanoFolder: 0.231 Positive Predictive Value CentroidAlifold(seed): 0.925 NanoFolder: 0.178 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	114 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.743 NanoFolder: 0.191 Sensitivity PETfold_pre2.0(20): 0.646 NanoFolder: 0.221 Positive Predictive Value PETfold_pre2.0(20): 0.857 NanoFolder: 0.169 Number of pairs reference - predicted secondary structure: 114 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.731 NanoFolder: 0.189 Sensitivity CentroidAlifold(20): 0.584 NanoFolder: 0.218 Positive Predictive Value CentroidAlifold(20): 0.917 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	248 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.679 NanoFolder: 0.198 Sensitivity CentroidHomfold‑LAST: 0.527 NanoFolder: 0.233 Positive Predictive Value CentroidHomfold‑LAST: 0.876 NanoFolder: 0.171 Number of pairs reference - predicted secondary structure: 248 Wilcoxon single-rank test P-value: 3.56938820447e-08	113 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.735 NanoFolder: 0.192 Sensitivity PPfold(20): 0.619 NanoFolder: 0.221 Positive Predictive Value PPfold(20): 0.873 NanoFolder: 0.170 Number of pairs reference - predicted secondary structure: 113 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.684 NanoFolder: 0.189 Sensitivity RNAalifold(20): 0.554 NanoFolder: 0.218 Positive Predictive Value RNAalifold(20): 0.846 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.664 NanoFolder: 0.202 Sensitivity MXScarna(seed): 0.566 NanoFolder: 0.232 Positive Predictive Value MXScarna(seed): 0.780 NanoFolder: 0.179 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.683 NanoFolder: 0.189 Sensitivity MXScarna(20): 0.614 NanoFolder: 0.218 Positive Predictive Value MXScarna(20): 0.761 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.671 NanoFolder: 0.194 Sensitivity IPknot: 0.616 NanoFolder: 0.229 Positive Predictive Value IPknot: 0.731 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	108 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.659 NanoFolder: 0.193 Sensitivity Multilign(20): 0.586 NanoFolder: 0.222 Positive Predictive Value Multilign(20): 0.743 NanoFolder: 0.171 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 3.56938820447e-08	104 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.591 NanoFolder: 0.197 Sensitivity Murlet(20): 0.450 NanoFolder: 0.227 Positive Predictive Value Murlet(20): 0.778 NanoFolder: 0.174 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.544 NanoFolder: 0.201 Sensitivity RNAalifold(seed): 0.340 NanoFolder: 0.231 Positive Predictive Value RNAalifold(seed): 0.873 NanoFolder: 0.178 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.619 NanoFolder: 0.194 Sensitivity CentroidFold: 0.569 NanoFolder: 0.229 Positive Predictive Value CentroidFold: 0.676 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	71 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.672 NanoFolder: 0.235 Sensitivity RNASampler(20): 0.506 NanoFolder: 0.278 Positive Predictive Value RNASampler(20): 0.893 NanoFolder: 0.202 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.603 NanoFolder: 0.194 Sensitivity Contrafold: 0.591 NanoFolder: 0.229 Positive Predictive Value Contrafold: 0.618 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.583 NanoFolder: 0.194 Sensitivity Sfold: 0.531 NanoFolder: 0.229 Positive Predictive Value Sfold: 0.641 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.720 NanoFolder: 0.328 Sensitivity Multilign(seed): 0.639 NanoFolder: 0.402 Positive Predictive Value Multilign(seed): 0.813 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	251 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.586 NanoFolder: 0.194 Sensitivity MaxExpect: 0.570 NanoFolder: 0.229 Positive Predictive Value MaxExpect: 0.604 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.585 NanoFolder: 0.194 Sensitivity ProbKnot: 0.577 NanoFolder: 0.229 Positive Predictive Value ProbKnot: 0.595 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.557 NanoFolder: 0.194 Sensitivity Fold: 0.556 NanoFolder: 0.229 Positive Predictive Value Fold: 0.560 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.526 NanoFolder: 0.315 Sensitivity RNASampler(seed): 0.356 NanoFolder: 0.382 Positive Predictive Value RNASampler(seed): 0.782 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.66763272401e-08	251 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.556 NanoFolder: 0.194 Sensitivity UNAFold: 0.549 NanoFolder: 0.229 Positive Predictive Value UNAFold: 0.566 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	248 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.547 NanoFolder: 0.198 Sensitivity RNAsubopt: 0.551 NanoFolder: 0.233 Positive Predictive Value RNAsubopt: 0.546 NanoFolder: 0.171 Number of pairs reference - predicted secondary structure: 248 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.482 NanoFolder: 0.189 Sensitivity RSpredict(20): 0.342 NanoFolder: 0.218 Positive Predictive Value RSpredict(20): 0.682 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	114 CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.525 NanoFolder: 0.187 Sensitivity CMfinder(20): 0.353 NanoFolder: 0.216 Positive Predictive Value CMfinder(20): 0.783 NanoFolder: 0.165 Number of pairs reference - predicted secondary structure: 114 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.542 NanoFolder: 0.194 Sensitivity PknotsRG: 0.540 NanoFolder: 0.229 Positive Predictive Value PknotsRG: 0.546 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.464 NanoFolder: 0.189 Sensitivity Carnac(20): 0.244 NanoFolder: 0.218 Positive Predictive Value Carnac(20): 0.884 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.550 NanoFolder: 0.194 Sensitivity RNAfold: 0.547 NanoFolder: 0.229 Positive Predictive Value RNAfold: 0.555 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 CMfinder(seed) vs NanoFolder Matthews Correlation Coefficient CMfinder(seed): 0.454 NanoFolder: 0.216 Sensitivity CMfinder(seed): 0.267 NanoFolder: 0.252 Positive Predictive Value CMfinder(seed): 0.774 NanoFolder: 0.188 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	160 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.559 NanoFolder: 0.188 Sensitivity Afold: 0.551 NanoFolder: 0.218 Positive Predictive Value Afold: 0.569 NanoFolder: 0.165 Number of pairs reference - predicted secondary structure: 160 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.656 NanoFolder: 0.339 Sensitivity HotKnots: 0.650 NanoFolder: 0.391 Positive Predictive Value HotKnots: 0.668 NanoFolder: 0.302 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.505 NanoFolder: 0.194 Sensitivity CRWrnafold: 0.503 NanoFolder: 0.229 Positive Predictive Value CRWrnafold: 0.509 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.604 NanoFolder: 0.390 Sensitivity Pknots: 0.590 NanoFolder: 0.447 Positive Predictive Value Pknots: 0.625 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.479 NanoFolder: 0.194 Sensitivity McQFold: 0.464 NanoFolder: 0.229 Positive Predictive Value McQFold: 0.496 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.491 NanoFolder: 0.200 Sensitivity RNAshapes: 0.482 NanoFolder: 0.235 Positive Predictive Value RNAshapes: 0.502 NanoFolder: 0.173 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 PPfold(seed) vs NanoFolder Matthews Correlation Coefficient PPfold(seed): 0.599 NanoFolder: 0.368 Sensitivity PPfold(seed): 0.383 NanoFolder: 0.429 Positive Predictive Value PPfold(seed): 0.939 NanoFolder: 0.322 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.74569091494e-09	116 Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.322 NanoFolder: 0.189 Sensitivity Mastr(20): 0.125 NanoFolder: 0.218 Positive Predictive Value Mastr(20): 0.832 NanoFolder: 0.167 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.470 NanoFolder: 0.261 Sensitivity Murlet(seed): 0.254 NanoFolder: 0.304 Positive Predictive Value Murlet(seed): 0.871 NanoFolder: 0.229 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	233 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.479 NanoFolder: 0.205 Sensitivity RNASLOpt: 0.446 NanoFolder: 0.239 Positive Predictive Value RNASLOpt: 0.517 NanoFolder: 0.178 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	110 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.562 NanoFolder: 0.341 Sensitivity Cylofold: 0.530 NanoFolder: 0.392 Positive Predictive Value Cylofold: 0.602 NanoFolder: 0.306 Number of pairs reference - predicted secondary structure: 110 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.395 NanoFolder: 0.194 Sensitivity RNAwolf: 0.405 NanoFolder: 0.229 Positive Predictive Value RNAwolf: 0.386 NanoFolder: 0.168 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	246 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.348 NanoFolder: 0.200 Sensitivity Vsfold4: 0.318 NanoFolder: 0.236 Positive Predictive Value Vsfold4: 0.384 NanoFolder: 0.173 Number of pairs reference - predicted secondary structure: 246 Wilcoxon single-rank test P-value: 3.56938820447e-08	244 Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.334 NanoFolder: 0.201 Sensitivity Vsfold5: 0.314 NanoFolder: 0.236 Positive Predictive Value Vsfold5: 0.358 NanoFolder: 0.174 Number of pairs reference - predicted secondary structure: 244 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.573 NanoFolder: 0.390 Sensitivity Alterna: 0.561 NanoFolder: 0.447 Positive Predictive Value Alterna: 0.593 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 RDfolder vs NanoFolder Matthews Correlation Coefficient RDfolder: 0.477 NanoFolder: 0.390 Sensitivity RDfolder: 0.419 NanoFolder: 0.447 Positive Predictive Value RDfolder: 0.550 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.260 Carnac(seed): 0.257 Sensitivity NanoFolder: 0.303 Carnac(seed): 0.073 Positive Predictive Value NanoFolder: 0.226 Carnac(seed): 0.911 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.339915559821	104 MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.456 NanoFolder: 0.352 Sensitivity MCFold: 0.509 NanoFolder: 0.404 Positive Predictive Value MCFold: 0.416 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 RSpredict(seed) vs NanoFolder Matthews Correlation Coefficient RSpredict(seed): 0.236 NanoFolder: 0.201 Sensitivity RSpredict(seed): 0.105 NanoFolder: 0.231 Positive Predictive Value RSpredict(seed): 0.535 NanoFolder: 0.178 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.201 Mastr(seed): 0.070 Sensitivity NanoFolder: 0.232 Mastr(seed): 0.007 Positive Predictive Value NanoFolder: 0.178 Mastr(seed): 0.673 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08
Mastr(seed)	51 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.791 Mastr(seed): 0.371 Sensitivity TurboFold(seed): 0.762 Mastr(seed): 0.166 Positive Predictive Value TurboFold(seed): 0.822 Mastr(seed): 0.829 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	626 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.739 Mastr(seed): 0.115 Sensitivity PETfold_pre2.0(seed): 0.656 Mastr(seed): 0.016 Positive Predictive Value PETfold_pre2.0(seed): 0.833 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 626 Wilcoxon single-rank test P-value: 3.56938820447e-08	644 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.796 Mastr(seed): 0.113 Sensitivity ContextFold: 0.762 Mastr(seed): 0.016 Positive Predictive Value ContextFold: 0.831 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08	343 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.783 Mastr(seed): 0.106 Sensitivity TurboFold(20): 0.736 Mastr(seed): 0.014 Positive Predictive Value TurboFold(20): 0.834 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 343 Wilcoxon single-rank test P-value: 3.56938820447e-08	618 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.714 Mastr(seed): 0.114 Sensitivity CentroidAlifold(seed): 0.568 Mastr(seed): 0.016 Positive Predictive Value CentroidAlifold(seed): 0.899 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 618 Wilcoxon single-rank test P-value: 3.56938820447e-08	342 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Mastr(seed): 0.105 Sensitivity PETfold_pre2.0(20): 0.639 Mastr(seed): 0.013 Positive Predictive Value PETfold_pre2.0(20): 0.855 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 342 Wilcoxon single-rank test P-value: 3.56938820447e-08	345 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.726 Mastr(seed): 0.104 Sensitivity CentroidAlifold(20): 0.570 Mastr(seed): 0.013 Positive Predictive Value CentroidAlifold(20): 0.926 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08	628 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 Mastr(seed): 0.117 Sensitivity CentroidHomfold‑LAST: 0.569 Mastr(seed): 0.017 Positive Predictive Value CentroidHomfold‑LAST: 0.870 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 628 Wilcoxon single-rank test P-value: 3.56938820447e-08	331 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.736 Mastr(seed): 0.108 Sensitivity PPfold(20): 0.619 Mastr(seed): 0.014 Positive Predictive Value PPfold(20): 0.876 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 331 Wilcoxon single-rank test P-value: 3.56938820447e-08	345 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.664 Mastr(seed): 0.104 Sensitivity RNAalifold(20): 0.527 Mastr(seed): 0.013 Positive Predictive Value RNAalifold(20): 0.836 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08	640 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.646 Mastr(seed): 0.113 Sensitivity MXScarna(seed): 0.555 Mastr(seed): 0.016 Positive Predictive Value MXScarna(seed): 0.754 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 640 Wilcoxon single-rank test P-value: 3.56938820447e-08	345 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.691 Mastr(seed): 0.104 Sensitivity MXScarna(20): 0.615 Mastr(seed): 0.013 Positive Predictive Value MXScarna(20): 0.778 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08	644 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.658 Mastr(seed): 0.113 Sensitivity IPknot: 0.606 Mastr(seed): 0.016 Positive Predictive Value IPknot: 0.714 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.654 Mastr(seed): 0.112 Sensitivity Multilign(20): 0.578 Mastr(seed): 0.015 Positive Predictive Value Multilign(20): 0.742 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.585 Mastr(seed): 0.125 Sensitivity Murlet(20): 0.434 Mastr(seed): 0.019 Positive Predictive Value Murlet(20): 0.791 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	608 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.550 Mastr(seed): 0.115 Sensitivity RNAalifold(seed): 0.359 Mastr(seed): 0.016 Positive Predictive Value RNAalifold(seed): 0.845 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 608 Wilcoxon single-rank test P-value: 3.56938820447e-08	643 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.637 Mastr(seed): 0.114 Sensitivity CentroidFold: 0.587 Mastr(seed): 0.016 Positive Predictive Value CentroidFold: 0.692 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.606 Mastr(seed): 0.187 Sensitivity RNASampler(20): 0.406 Mastr(seed): 0.043 Positive Predictive Value RNASampler(20): 0.905 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	644 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.622 Mastr(seed): 0.113 Sensitivity Contrafold: 0.608 Mastr(seed): 0.016 Positive Predictive Value Contrafold: 0.637 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08	644 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.613 Mastr(seed): 0.113 Sensitivity Sfold: 0.563 Mastr(seed): 0.016 Positive Predictive Value Sfold: 0.670 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.698 Mastr(seed): 0.491 Sensitivity Multilign(seed): 0.660 Mastr(seed): 0.299 Positive Predictive Value Multilign(seed): 0.741 Mastr(seed): 0.809 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	644 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.601 Mastr(seed): 0.113 Sensitivity MaxExpect: 0.587 Mastr(seed): 0.016 Positive Predictive Value MaxExpect: 0.618 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08	644 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.599 Mastr(seed): 0.113 Sensitivity ProbKnot: 0.590 Mastr(seed): 0.016 Positive Predictive Value ProbKnot: 0.610 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08	644 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.580 Mastr(seed): 0.113 Sensitivity Fold: 0.578 Mastr(seed): 0.016 Positive Predictive Value Fold: 0.582 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.629 Mastr(seed): 0.512 Sensitivity RNASampler(seed): 0.468 Mastr(seed): 0.322 Positive Predictive Value RNASampler(seed): 0.847 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	644 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.582 Mastr(seed): 0.113 Sensitivity UNAFold: 0.574 Mastr(seed): 0.016 Positive Predictive Value UNAFold: 0.592 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08	628 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.573 Mastr(seed): 0.117 Sensitivity RNAsubopt: 0.575 Mastr(seed): 0.017 Positive Predictive Value RNAsubopt: 0.572 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 628 Wilcoxon single-rank test P-value: 3.56938820447e-08	345 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.453 Mastr(seed): 0.104 Sensitivity RSpredict(20): 0.313 Mastr(seed): 0.013 Positive Predictive Value RSpredict(20): 0.657 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08	339 CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.526 Mastr(seed): 0.107 Sensitivity CMfinder(20): 0.358 Mastr(seed): 0.014 Positive Predictive Value CMfinder(20): 0.774 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 339 Wilcoxon single-rank test P-value: 3.56938820447e-08	642 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.575 Mastr(seed): 0.114 Sensitivity PknotsRG: 0.571 Mastr(seed): 0.016 Positive Predictive Value PknotsRG: 0.580 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 642 Wilcoxon single-rank test P-value: 3.56938820447e-08	345 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.398 Mastr(seed): 0.104 Sensitivity Carnac(20): 0.180 Mastr(seed): 0.013 Positive Predictive Value Carnac(20): 0.881 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08	644 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.577 Mastr(seed): 0.113 Sensitivity RNAfold: 0.572 Mastr(seed): 0.016 Positive Predictive Value RNAfold: 0.583 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 644 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.486 Mastr(seed): 0.312 Sensitivity CMfinder(seed): 0.312 Mastr(seed): 0.118 Positive Predictive Value CMfinder(seed): 0.757 Mastr(seed): 0.828 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	502 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.564 Mastr(seed): 0.123 Sensitivity Afold: 0.559 Mastr(seed): 0.019 Positive Predictive Value Afold: 0.571 Mastr(seed): 0.821 Number of pairs reference - predicted secondary structure: 502 Wilcoxon single-rank test P-value: 3.56938820447e-08	231 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.677 Mastr(seed): 0.266 Sensitivity HotKnots: 0.677 Mastr(seed): 0.091 Positive Predictive Value HotKnots: 0.680 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 231 Wilcoxon single-rank test P-value: 3.56938820447e-08	641 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.509 Mastr(seed): 0.115 Sensitivity CRWrnafold: 0.505 Mastr(seed): 0.016 Positive Predictive Value CRWrnafold: 0.514 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	158 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.533 Mastr(seed): 0.307 Sensitivity Pknots: 0.528 Mastr(seed): 0.117 Positive Predictive Value Pknots: 0.545 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 158 Wilcoxon single-rank test P-value: 3.56938820447e-08	641 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.479 Mastr(seed): 0.115 Sensitivity McQFold: 0.462 Mastr(seed): 0.016 Positive Predictive Value McQFold: 0.498 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	605 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.528 Mastr(seed): 0.115 Sensitivity RNAshapes: 0.518 Mastr(seed): 0.016 Positive Predictive Value RNAshapes: 0.540 Mastr(seed): 0.812 Number of pairs reference - predicted secondary structure: 605 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.626 Mastr(seed): 0.324 Sensitivity PPfold(seed): 0.495 Mastr(seed): 0.125 Positive Predictive Value PPfold(seed): 0.794 Mastr(seed): 0.845 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	345 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.265 Mastr(seed): 0.104 Sensitivity Mastr(20): 0.085 Mastr(seed): 0.013 Positive Predictive Value Mastr(20): 0.834 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 345 Wilcoxon single-rank test P-value: 3.56938820447e-08	122 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.530 Mastr(seed): 0.370 Sensitivity Murlet(seed): 0.336 Mastr(seed): 0.168 Positive Predictive Value Murlet(seed): 0.839 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 122 Wilcoxon single-rank test P-value: 3.56938820447e-08	587 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.479 Mastr(seed): 0.124 Sensitivity RNASLOpt: 0.446 Mastr(seed): 0.019 Positive Predictive Value RNASLOpt: 0.516 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 587 Wilcoxon single-rank test P-value: 3.56938820447e-08	215 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.520 Mastr(seed): 0.285 Sensitivity Cylofold: 0.495 Mastr(seed): 0.101 Positive Predictive Value Cylofold: 0.553 Mastr(seed): 0.807 Number of pairs reference - predicted secondary structure: 215 Wilcoxon single-rank test P-value: 3.56938820447e-08	641 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.394 Mastr(seed): 0.115 Sensitivity RNAwolf: 0.404 Mastr(seed): 0.016 Positive Predictive Value RNAwolf: 0.386 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 641 Wilcoxon single-rank test P-value: 3.56938820447e-08	615 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.334 Mastr(seed): 0.119 Sensitivity Vsfold4: 0.303 Mastr(seed): 0.017 Positive Predictive Value Vsfold4: 0.369 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 615 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.311 Mastr(seed): 0.120 Sensitivity Vsfold5: 0.292 Mastr(seed): 0.018 Positive Predictive Value Vsfold5: 0.335 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	157 Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.560 Mastr(seed): 0.309 Sensitivity Alterna: 0.552 Mastr(seed): 0.118 Positive Predictive Value Alterna: 0.575 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	157 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.485 Mastr(seed): 0.309 Sensitivity RDfolder: 0.420 Mastr(seed): 0.118 Positive Predictive Value RDfolder: 0.569 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	268 Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.215 Mastr(seed): 0.192 Sensitivity Carnac(seed): 0.055 Mastr(seed): 0.045 Positive Predictive Value Carnac(seed): 0.850 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 268 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.473 Mastr(seed): 0.261 Sensitivity MCFold: 0.525 Mastr(seed): 0.084 Positive Predictive Value MCFold: 0.433 Mastr(seed): 0.822 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	620 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.235 Mastr(seed): 0.115 Sensitivity RSpredict(seed): 0.111 Mastr(seed): 0.016 Positive Predictive Value RSpredict(seed): 0.500 Mastr(seed): 0.820 Number of pairs reference - predicted secondary structure: 620 Wilcoxon single-rank test P-value: 3.56938820447e-08	126 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.201 Mastr(seed): 0.070 Sensitivity NanoFolder: 0.232 Mastr(seed): 0.007 Positive Predictive Value NanoFolder: 0.178 Mastr(seed): 0.673 Number of pairs reference - predicted secondary structure: 126 Wilcoxon single-rank test P-value: 3.56938820447e-08

Matthews Correlation Coefficients (MCC) plotted for all methods in a ranking. MCCs were calculated by taking into account all reference and predicted RNA structures by a given method in the entire ranking. The plot includes only methods for which at least 40% of comparisons with other methods is valid (i.e. at least 40% of the comparisons were based on more than 10 predictions for common targets).